HIPAA compliant payment processing for therapists: integrated EHR payments vs Stripe, Square, and Ivy Pay (2026)

Taking a card payment is the easy part of running a therapy practice. HIPAA compliant payment processing for therapists in 2026 is really about everything around the card. Does the platform that stores the invoice sign a business associate agreement? What does processing actually cost each month? And does the workflow fit how therapy is paid for, with cards on file, automatic charges after sessions, and HSA and FSA cards?

This guide compares seven EHRs with built in payments and three standalone processors on five things: the BAA, the card rate and any monthly fee, HSA and FSA acceptance, card on file and autopay, and what the client sees. Every figure comes from the vendor's own pricing, help, and legal pages. If your question is about claims and invoicing software rather than card acceptance, start with the billing software comparison and come back here for the payments side.

The short version: the processor moves the money, the platform that holds the client record signs the BAA, and your practice still decides how that record is handled.

How we chose these options

We compared the seven EHRs therapists most often weigh when they want payments inside the same system as notes and scheduling, plus the three standalone processors that come up whenever a therapist asks how to take card payments without an EHR. SimplePractice and TherapyNotes are the established names, Sessions Health, TheraNest, and TheraPlatform the lower cost options, Jane the usual pick for multidisciplinary clinics, and Upheal is included because its client payments are built in. The page says where each competitor beats it.

For each option we read the vendor's own pricing, help center, and legal pages. We checked the card rate, any fee for payments, the processor underneath, the BAA, HSA and FSA acceptance, card on file and autopay, the client portal, payout timing, and whether the vendor's AI does any billing work. Where a vendor publishes nothing on a point, the table says so rather than guessing.

Last verified 15 October 2026.

Do therapy payment processors need a HIPAA BAA?

Generally no, as long as the processor only processes payments. The card processor itself does not need to sign a business associate agreement with your practice, but the platform that stores your invoices, balances, and client details does. The U.S. Department of Health and Human Services lists payment processing among the situations where no BAA is required. When a financial institution processes card transactions, clears checks, or moves funds to pay for health care, it is providing normal banking services to its customer, not acting on behalf of the covered entity. The same guidance names billing and practice management as business associate work, so a payments vendor that also sends your invoices, tracks balances, or stores client details does need a BAA. Read the exception on the HHS business associates page.

That is why Stripe, the processor underneath six of the seven EHRs here, publishes no BAA, and why its services agreement tells users not to send it protected health information at all. The processor only needs the card, the amount, and a merchant name. Everything else about the session stays with you.

So what does HIPAA compliant payment processing actually mean for a therapy practice? Five things, in order of how often they go wrong.

1. A BAA with the system that holds the record. Your EHR, invoicing tool, or scheduling app stores names, dates of service, diagnosis codes on superbills, and balances. That is protected health information, and that vendor must sign a BAA. Every EHR on this page does. Among the standalone options, Square accepts a BAA through its terms, Ivy Pay signs one at signup, and Stripe offers none.
2. Card security handled by the processor. The processor handles most of PCI DSS, the card industry standard: Stripe, Square, and CardConnect tokenize the card so your practice never stores a card number. Your part is to use their hosted forms, not to write card numbers down, and to complete any PCI questionnaire your processor asks for.
3. No clinical detail on receipts, statement descriptors, or memo lines. A receipt that says "Therapy session, F41.1" is a disclosure. The amount, date, and your practice name are enough. The same rule applies to the memo field in any payment app.
4. Access controls and an audit trail on the billing record. Who in your practice can see balances and card details, and whether changes are logged, is a HIPAA question even when the card itself is safe.
5. A business account, never a personal payment app. Personal Venmo, Zelle, and PayPal accounts are built for payments between people who know each other, with social feeds and memo lines that were never designed for health care. The FAQ below covers each one.

HIPAA compliant payment processing for therapists, compared

The first table covers payments inside an EHR, the second covers the standalone processors. Each cell is a short summary; the vendor profiles below carry the detail. Every figure was read on the vendor's own pages on 15 October 2026.

Verified against each vendor's own pricing, help, and legal pages on 15 October 2026. ✓ = included · ◑ = partial or limited · Not published = the vendor's own pages do not say. AI notes add ons are priced per clinician a month. Jane prices in USD.

Verified on each vendor's own pricing, help, and legal pages on 15 October 2026. ✓ = included · ✗ = not available · Not published = the vendor's own pages do not say. Stripe's higher rate covers cards typed into its Dashboard or taken by phone, and saved cards first entered that way.

Upheal

Upheal is an AI native EHR for mental health practices, and client payments are built into the same platform that writes your notes. The card is collected in the intake form, the charge happens after the session, and the receipt, the balance, and the superbill all live next to the note they came from.

Compliance and BAA. Upheal publishes its full Business Associate Agreement, effective March 25, 2026, and providers accept it during signup, before any PHI enters the platform. One agreement covers the providers in your practice. Card payments in Upheal run through Stripe, the secure payment processing service we use; you set up Stripe from inside Upheal, and no session detail goes to the processor. Upheal is HIPAA, PHIPA, PIPEDA, GDPR, and DPA compliant, has completed a SOC 2 Type II audit, and is continuously externally tested.

Rate and payments fee. Card payments are 2.9% + $0.30 per transaction. There is no separate payment app and no extra subscription: payments are part of the EHR plan at $1 per session, or EHR Pro at $99 a month flat, which adds Assistant Pro. Clients can pay with HSA and FSA cards; they are processed like any other card through Stripe, and whether a given charge is approved is up to the client's card issuer and plan administrator.

Card on file, autopay, and portal. Add card collection to your intake forms; the card is saved during onboarding, so there is no separate payment step before the first session. Clients authorize automatic payments and add their card through the same form. Turn on automatic payments and choose when they run, and Upheal charges the saved card and sends the receipt. In the Client Portal, clients can view invoices and superbills, check what they owe, pay online, and update their own card.

Upheal Assistant. Separate from the payment features, the Upheal Assistant handles the follow up. Its daily billing wrap-up checks overdue invoices, failed charges, uninvoiced sessions, and card issues, and suggests one next step for you to approve. Declined cards are retried with a drafted message and a fresh payment link, and aging balances get a reminder. Ask it in a sentence for your outstanding client balances, to create and send an invoice, or to generate a superbill, and see everything else it does in the Assistant jobs library. The Assistant comes with every plan with a monthly usage limit; Assistant Pro, $39 a month and included in EHR Pro, removes the limit.

Receipts and records. Superbills are generated from the signed note with ICD-10 and CPT codes in place, and shared with clients automatically through the Client Portal. Log cash, checks, Venmo, Zelle, or a card run outside Upheal, and the invoice is marked paid without emailing the client, which matters most in the month you switch. The payments rebuild earlier this year is covered in what's new in Upheal payments.

Best for and trade off. Upheal fits a therapist who wants payments and notes in one system, with AI included rather than added per clinician, and who pays per session rather than per seat. The honest limits: client payments are available in the US and Canada, Upheal does not publish a payout schedule (you set it in Stripe), and Jane's integrated rate is lower.

See how Upheal's client payments work, from intake card to paid balance.

SimplePractice

SimplePractice includes payments on every plan, charges one rate for online, saved, and in person cards, and lets clients pay in full or in part in its portal.

Compliance and BAA. You agree to SimplePractice's Business Associate Agreement when you create the trial account, and the agreement is published on its site. Processing runs on Stripe through an online payments account that SimplePractice's risk team verifies in two to three business days.

Rate and payments fee. 3.15% + $0.30 per successful transaction, one rate for every card, whether it is charged online, stored, or tapped in person through the mobile app. Payments come with every plan rather than as an add on, so the plan is what you pay to take cards: Starter at $49, Essential at $79, or Plus at $99 a month, plus $20 a year per clinician for the AMA CPT license. Text payment links are a Plus feature.

Card on file, autopay, and portal. AutoPay charges the default card for the full invoiced amount overnight, and three failed nights turn it off for that client. The portal's card form has no signature box, so SimplePractice recommends a separate credit card authorization form. Clients can view invoices, statements, and superbills, pay the full balance or a single invoice in full or in part, and add a card, but they cannot edit or remove one.

HSA, FSA, and payouts. Accounts are assigned an HSA/FSA eligible merchant code automatically. Payouts run daily and include charges from two business days earlier, with a seven day hold on the first payout and no instant option.

Best for and trade off. Practices that want one card rate everywhere and partial payments in the portal, at the highest integrated rate on this page. See the full Upheal vs SimplePractice comparison.

TherapyNotes

TherapyNotes is the billing first EHR here, and its payments follow the same pattern: a traditional merchant account with a bank processor rather than a Stripe account.

Compliance and BAA. Since 23 April 2026 the BAA is built directly into TherapyNotes' terms of service, so there is nothing to sign. Processing runs through CardConnect, a Fiserv company, and you apply for a merchant account separately; approval takes up to five business days.

Rate and payments fee. 3.1% + $0.30 per transaction, one rate for Visa, Mastercard, Discover, American Express, and HSA and FSA cards. Card processing is an optional feature on the $69 Solo plan ($79 plus $50 per added clinician for groups), with no monthly processing fee published. Two other fees are published: $35 per chargeback, and $29.95 a month if you skip the PCI compliance questionnaire. Processing is not free during the trial.

Card on file, autopay, and portal. Cards are tokenized and stored, AutoPay charges outstanding balances overnight, and clients authorize it electronically through a payment authorization form in the portal. In the portal they can pay the full balance or a partial amount; a card entered there is not saved for the practice unless the client fills in the authorization form.

HSA, FSA, and payouts. HSA and FSA cards are accepted, though TherapyNotes does not recommend using an HSA card for AutoPay. Deposits land the next day for transactions before 9:30 pm Eastern.

Best for and trade off. Next day deposits in a billing focused EHR, with a separate merchant application and two fees to watch.

Sessions Health

Sessions Health has a free plan for up to three clients, and its $39 Professional plan ties TheraPlatform's Basic plan as the lowest paid plan with payments included. It passes on Stripe's standard rate with nothing added.

Compliance and BAA. The BAA is published and takes effect when you sign up. You connect your own Stripe account to Sessions Health, so you own the processor relationship and the payout settings.

Rate and payments fee. Stripe's 2.9% + $0.30 per successful card transaction, with no additional platform fee from Sessions Health. Online payments are included on the $39 Professional plan and on the free plan for up to three clients; each added practitioner is $29 a month. There is no annual plan.

Card on file, autopay, and portal. Clients save a card and sign a credit card authorization form in the portal. AutoPay runs daily at 12:30 am for any open bill on clients where it is enabled. In the portal, clients pay open invoices, add, remove, or relabel cards, and see statements and superbills.

HSA, FSA, and payouts. Sessions Health sets up the business classification that lets HSA and FSA cards go through, but says plainly that some will be declined. Stripe's standard payout timing applies: the first payout takes five to ten days, then two to four days.

Best for and trade off. A solo therapist who wants a low subscription and Stripe's own rate. The trade off is that the extras, from telehealth to AI notes, are add ons.

TheraNest (Ensora Health)

TheraNest, now sold by Ensora Health, has the lowest entry price on this page and a payments setup that changed in 2026.

Compliance and BAA. The BAA is an attachment inside Ensora's master subscription terms, which you accept as a covered entity; there is no standalone BAA page. Processing runs on Stripe through Ensora Payments, which means a new Stripe merchant account created for the practice; an existing Stripe account cannot be linked, and the older Vantage processor is being phased out.

Rate and payments fee. 2.99% + $0.30 per transaction on all three plans, with a footnote that additional fees may apply. Plans are $29, $59, and $89 per therapist a month, plus a mandatory $19.50 a year AMA CPT license fee. Payment processing is an add on subscription you enroll in on any plan, and Ensora publishes its per transaction rate but no monthly price for the add on. No in person rate is published, and USB card readers do not work with the Stripe based processor.

Card on file, autopay, and portal. Clients can save a card for future payments and staff can manage payment methods, but TheraNest does not publish an automatic charging feature or how consent is captured. In the portal, clients view and pay balances, see their payment history, and print invoices and superbills.

HSA, FSA, and payouts. HSA and FSA cards with a Visa, Mastercard, Discover, or American Express logo are accepted. Payout timing is stated three different ways across Ensora's pages, from thirty minutes to two business days; the help center figure is two business days after Stripe processes the payment, with the first payout taking up to fourteen business days.

Best for and trade off. The lowest plan price on this page, though you will need to confirm the payments add on price, the autopay story, and the payout timeline with Ensora.

TheraPlatform

TheraPlatform includes card processing on every plan, including the $39 Basic plan, and routes everything through the practice's own Stripe account.

Compliance and BAA. TheraPlatform provides and signs a business associate agreement at no charge. Payments run through Stripe Connect to a Stripe account you create, and TheraPlatform states that it adds no fee of its own.

Rate and payments fee. Not published. TheraPlatform's pricing, feature, and help pages say only that Stripe's fees apply, so you will pay whatever Stripe charges your account; at Stripe's standard rate that is 2.9% + $0.30. Plans are Basic $39, Pro $69, and Pro Plus $79 a month. AutoPay, payment reminders, and automated invoicing start at Pro; an in person terminal is Pro Plus only.

Card on file, autopay, and portal. Cards are stored at Stripe and clients enter them in the portal when billing is required. AutoPay is a practice wide setting with per client opt out on Pro and Pro Plus; the vendor does not describe how consent is collected. Clients make payments and view and print invoices and superbills in the portal.

HSA, FSA, and payouts. HSA and FSA cards are accepted, though the help center notes that a provider may need to ask Stripe to configure the account. Payouts are handled entirely by Stripe and TheraPlatform publishes no schedule.

Best for and trade off. Card processing on the cheapest plan and telehealth on every plan, with a rate you have to find in your own Stripe dashboard.

Jane

Jane is the multidisciplinary clinic pick, and on payments it has the lowest integrated rate on this page and publishes its in person rate, terminal price, and payout timing.

Compliance and BAA. Jane will enter into its standard Business Associate Agreement on request; it is not part of signup. Jane Payments runs on a Jane managed Stripe Express account, and a Stripe Standard account cannot be connected instead.

Rate and payments fee. 2.85% + $0.25 online and 2.6% + $0.10 in person, and Jane Payments carries no fee of its own on top of the plan. The terminal costs $239 until 31 October 2026 and $259 from 1 November. Plans in USD are Balance at $59 a month, which caps at 20 appointments, Practice at $79, and Thrive at $99, each for one practitioner. There is no free trial, and a Visa or Mastercard is required at signup.

Card on file, autopay, and portal. Cards are stored on file on every plan and can be charged after sessions by staff; automatic billing applies only to memberships. The intake form collects card details and consent to your cancellation policy. In the portal, clients pay their full balance and add a card.

HSA, FSA, and payouts. Jane sets merchant category 8099 automatically, so HSA and FSA cards work, with the caveat that approval depends on the card. Payouts run every two business days with a midnight Eastern cut off; instant payouts cost an extra 1.5%.

Best for and trade off. The best rate inside an EHR and strong scheduling, with autopay limited to memberships and no trial.

Standalone processors: Stripe, Square, and Ivy Pay

Use one of these when your notes and scheduling live somewhere without payments, or when you want a card reader in the room.

Stripe

Stripe is the engine behind six of the seven EHRs above, and you can use it directly through payment links and hosted invoices.

Compliance and BAA. Stripe publishes no BAA and asks users not to send it protected health information, as covered above. Stripe lists telehealth as a restricted business that needs extra due diligence, so expect questions during onboarding.

Rate and fees. 2.9% + $0.30 online, including a saved card the client entered, and 2.7% + $0.05 in person. A card you type into the Dashboard or take by phone costs 3.4% + $0.30, and so does a saved card first entered that way, per Stripe's page on manually entered payments. Stripe Invoicing adds 0.4% per paid invoice. ACH is 0.8% with a $5 cap. No monthly fee; a card reader is $59.

Card on file, HSA, FSA, and payouts. Saved cards require explicit client consent and a written record. HSA and FSA cards work for health care merchants with an eligible merchant code. Payouts take two business days, the first one seven to fourteen, and instant payouts cost 1.5%.

Best for and trade off. The cheapest way to add card links to a practice that already has an EHR without payments, at the cost of running two systems.

Square

Square is the pick when you want a reader on the desk and next day money.

Compliance and BAA. Square's HIPAA Business Associate Agreement is accepted through its general terms when you use its HIPAA enabled features, such as Appointments and Invoices, as a covered entity. Square handles PCI compliance on your behalf.

Rate and fees. On the free plan, 2.6% + $0.15 in person, 3.3% + $0.30 online and on invoices, and 3.5% + $0.15 when you key in a card or charge one saved on file; the $49 and $149 plans drop online to 2.9% + $0.30. ACH is 1% with a $1 minimum. A reader is $59 and a terminal $299.

Card on file, HSA, FSA, and payouts. Card on File needs written authorization from the client. Licensed health care providers can process HSA and FSA cards once the business category is set. Transfers land the next business day, or in minutes for 1.95%.

Best for and trade off. In person practices that want hardware and fast transfers, with the highest online rate on this page unless you pay for a plan.

Ivy Pay

Ivy Pay is a card on file app built for therapists, and it is the simplest option here.

Compliance and BAA. Ivy Pay signs a Business Associate Agreement at signup and runs as a payment services provider on top of its own processor and banking partners.

Rate and fees. 2.75% per charge, flat, for all major cards, with no fixed fee, no monthly fee, and no contract.

Card on file, HSA, FSA, and payouts. The client adds a debit, credit, HSA, or FSA card to a card profile, and you charge it after the session from the app. Deposits arrive as soon as the next day.

Best for and trade off. The lowest cost for online card payments on this page, with no client portal, no invoices or statements, text confirmations only, and no EHR integration, so every charge is a manual step.

What does card processing cost per month on each platform?

The rate is only one line. The honest comparison adds the subscription and multiplies the rate by a real month. Here is a solo therapist holding 50 sessions a month at $150, 40 of them paid by card, which is $6,000 of card volume and 40 charges, at the rates in force on 15 October 2026.

Rates and plan prices read on each vendor's own pages on 15 October 2026. SimplePractice ($20) and TheraNest ($19.50) charge a required yearly AMA CPT license fee per clinician, shown here as a monthly amount. Ensora publishes no price for TheraNest's payments add on, so that total is incomplete. Jane's Balance plan is excluded because it caps at 20 appointments a month. The three standalone lines exclude whatever the practice pays for notes, scheduling, and the client record elsewhere.

Ivy Pay is the cheapest way to take cards online, Square and Stripe cost less in person, and Jane has the lowest integrated rate. Between the EHRs the gap is mostly the subscription: Sessions Health and TherapyNotes differ by $12 in card fees and $30 in plan price. Sessions Health has the lowest EHR total with every fee published; TheraNest comes in about $3 under it before its payments add on.

Upheal's line includes AI notes, which the other EHRs add per clinician. On Upheal there are two plans: the EHR plan at $1 per session, and EHR Pro at $99 a month flat, which adds Assistant Pro.

Start free, no credit card required

Can clients pay for therapy with HSA or FSA cards?

Yes. Therapy received as medical treatment and amounts paid to a psychologist are qualified medical expenses, so clients can use a health savings account or flexible spending account to pay for it. The IRS lists both in its guide to deductible medical expenses, Publication 502, and the same definition governs what an HSA or FSA can reimburse.

In practice an HSA or FSA card runs on the major card networks, so it goes through the same processor as any other card. Two things decide whether a charge goes through. The first is your merchant category code: the card networks only allow HSA and FSA cards at merchants coded as health care, which is why SimplePractice, Jane, and Sessions Health say they set that code for you, and why Stripe says it is required. The second is the card issuer's own rules, which is why every vendor adds that approval is not guaranteed.

What the client needs from you is substantiation: a receipt or superbill with the date of service, the provider, and the service, in case the plan administrator asks. A receipt that shows only an amount may be sent back.

On Upheal, the client gets the receipt automatically, and the superbill from the signed note carries the codes an administrator may ask for.

Can I keep a card on file and charge clients automatically?

Yes, with the client's written authorization, and every EHR on this page can store a card; the differences are in who collects the consent and when the charge runs. Stripe and Square both require documented consent before a saved card is charged, and the EHRs build that consent into a form.

A card on file policy should state five things:

1. The fee or rate that will be charged.
2. When the charge happens: after the session, overnight, or on a schedule.
3. What is charged for a missed session or a late cancellation.
4. How the client updates or revokes the card.
5. What happens if a charge is declined.

Put the policy in the intake paperwork rather than in a message after the first session, so the authorization and the card arrive together.

On Upheal the authorization and the card come through the intake form, and the practice chooses when the charge runs, after the appointment or after the signed note. SimplePractice, TherapyNotes, and Sessions Health run AutoPay overnight on a fixed schedule; SimplePractice recommends a separate authorization form because its portal card form has no signature box. TheraPlatform limits AutoPay to its Pro plans, Jane automates only memberships, and TheraNest does not publish an automatic charging feature.

Keep the signed authorization on file, because it is your evidence if a client disputes a charge with their bank. Disputes cost money on top of the amount: Stripe charges $15 per dispute and TherapyNotes $35 per chargeback. A refund usually costs nothing to issue, but the original processing fee does not come back; Jane, PayPal, and Venmo all say so.

How do group practices collect client payments and track them across therapists?

One merchant account for the practice, per clinician attribution in reporting, and a client portal that posts each payment to the right balance. Those three things separate a group practice setup from a solo one, and they matter more than the rate: a $0.05 difference per transaction is small next to an afternoon of reconciling who saw whom.

Ask three questions of any platform. Does the payment post to the client's balance automatically, or does someone have to match it? Can a practice manager or biller work the balances without a clinical seat? And can you report collections by clinician for a pay period without exporting to a spreadsheet?

On Upheal, Reports has five dashboards and 30+ premade reports on sessions, billing, and payments, exportable as a spreadsheet, and Assistant Pro adds custom charts you describe in plain language. Pricing for group practices depends on the size of the practice, and associates are discounted; talk to sales for a quote. If your group also bills insurance, the companion guide to the best EHRs for therapists who accept insurance covers the claims side.

How to choose, and what to ask in a demo

Take the shortlist to a demo and ask these three questions. The answers separate platforms that take a card from platforms that run your billing.

1. Who signs the BAA, where is it, and what exactly does it cover? A platform that points you to its processor's security page has not answered.
2. What is my all in monthly cost at my session count: subscription, any payments fee, the percentage, and the fixed fee per charge, each stated separately?
3. Show me the client's side: how the card and the authorization are collected, what the receipt says, and what the client sees when a charge fails.

Frequently asked questions

What is HIPAA compliant payment processing?

It means taking card payments without exposing protected health information, with a business associate agreement in place with every vendor that stores your client records. A processor that only moves the money generally needs no BAA under HHS guidance, so compliance comes from the platform that holds invoices and client details, from keeping clinical detail off receipts and memo lines, and from using a business account rather than a personal payment app.

Is Stripe HIPAA compliant?

Stripe publishes no business associate agreement and asks users not to send it protected health information, which fits HHS guidance that a processor doing only payment processing is not a business associate. Practices use Stripe compliantly by sending it only the card, the amount, and a merchant name, and by keeping the client record in a platform that signs a BAA. That is how Upheal, SimplePractice, Sessions Health, TheraNest, TheraPlatform, and Jane all run on Stripe.

Is Square HIPAA compliant?

Square offers a HIPAA Business Associate Agreement, which covered entities accept through its terms when they use HIPAA enabled features such as Appointments and Invoices. Square handles PCI compliance on your behalf and lets licensed health care providers take HSA and FSA cards. Keep clinical detail out of item names and invoice notes, since those appear on receipts.

Is Venmo HIPAA compliant?

Venmo publishes no HIPAA page and no business associate agreement, and its personal accounts may not be used for business transactions. A therapy practice would need a Venmo business profile, which costs 1.9% + $0.10 per payment. The bigger problem is the feed. On Venmo's Public and Friends settings the payment note, both names, and the timestamp are shared, and new accounts may be set to public by default, so a client paying "therapy" to a named therapist is a disclosure. If a client insists on paying this way, use a business profile, keep the note blank, set the payment to private, and log it in your EHR as an external payment.

Is Zelle or PayPal HIPAA compliant?

Neither Zelle nor PayPal publishes a HIPAA page or a business associate agreement. Zelle is a bank to bank transfer for people you know and trust: payments cannot be reversed, there is no purchase protection, and whether a small business can receive Zelle at all depends on the bank. PayPal requires a business account for commercial activity and charges from 2.99% to receive payments for goods and services. It lists licensed health care services and telemedicine among the categories that need its approval first, and its invoicing terms say HIPAA covered entities must not send protected health information through PayPal Invoicing. The compliance question is the same as for any processor: a business account, nothing clinical in the memo, and the record of the payment in your EHR.

What is the cheapest way to accept card payments as a therapist?

Ivy Pay's flat 2.75% is the cheapest way on this page to take cards online, and Jane's 2.85% + $0.25 is the cheapest online rate inside an EHR. In person, Jane, Square, and Stripe all cost less per charge. For a therapist who also needs notes, scheduling, and a client portal, the subscription matters more than the rate: on 40 card payments a month the fees differ by a few dollars between platforms, while plans differ by $30 or more. Compare the monthly total, not the percentage.

Can I pass card processing fees to clients?

Sometimes: processors that allow a surcharge limit it to credit cards and cap it at 3%, never on debit, prepaid, HSA, or FSA cards, and some states ban it. Square supports credit card surcharges in an open beta, and Stripe only through a developer integration. Of the EHRs on this page, SimplePractice is the only one that documents a way to do it, as a manual line item on the invoice, with its own warning that surcharging is illegal in some states. Check your state's rules first, state the surcharge in your fee policy, and never add one to an HSA or FSA card.

Does Upheal have integrated payment processing?

Yes. Upheal includes card payments, invoicing, superbills, and balance tracking in the EHR, at 2.9% + $0.30 per transaction with no separate payments app or fee. Payments are part of the EHR plan at $1 per session or EHR Pro at $99 a month, clients pay and update their card in the Client Portal, and HSA and FSA cards are processed like any other card. Client payments are available in the US and Canada.

Do I need a separate merchant account to take card payments in my EHR?

Usually not: six of the seven EHRs here set up card processing inside the platform through Stripe, while TherapyNotes requires a separate merchant application with CardConnect. Upheal, SimplePractice, Sessions Health, TheraPlatform, TheraNest, and Jane all run on Stripe, though SimplePractice's risk team takes two to three business days to verify a new account. TherapyNotes' merchant application takes up to five business days to approve.

Payments that live next to the note

Whichever option you choose, the processor should see nothing but the card and the amount, and the record of each payment should sit with the session it paid for. Judge the option you are considering on who signs the BAA, on the monthly total rather than the rate, and on what your client sees when a card fails.

If you want the card collected at intake, charged after the session, and reconciled against the note in the same place as your AI notes, try Upheal free and take your first card payment from the Client Portal.

Sources: each vendor's own pricing, help center, and legal pages, checked on 15 October 2026, the HHS business associates guidance, IRS Publication 502, and Stripe's page on manually entered payments. Pricing and features change; confirm current terms with each vendor before deciding.