A medical or dental practice does not take one kind of card payment. It takes small copays at the front desk, balances after insurance, and larger treatment payments by phone or invoice. Each one has a different price on a flat-rate account, so the cheapest setup is the one that fits your own mix. This guide shows a made-up month, the Stripe and Square prices as read on their own pages on November 13, 2026, and a plain how-to on keyed-in cards, saved cards and patient payment links.
The short answer
- Count your payments by type first. Copays in person, balances paid online or by link, and larger payments typed in over the phone are priced differently. The average ticket in each group matters more than the total.
- Typing in a card costs more than a tap. As read on Square’s fees page on November 13, 2026, manual entry or card on file is 3.5% + 15 cents, against 2.6% + 15 cents for tap, dip or swipe. As read on Stripe’s pricing page the same day, manually entered cards carry an extra 0.5%.
- Our study is a model. NPS’s 2026 pricing study finds interchange pass-through costs 19% to 31% less than flat rate for online and invoice sales across average tickets from $15 to $2,500. NPS sells pass-through, so we are not neutral. Treat it as a reason to get a quote.
- Flat rate can still win in places. The study says it can for very small in-person tickets, around $15 and under, and for brand-new, very low-volume businesses.
- This page is about card fees only. It is not about HIPAA or any other medical, privacy or legal rule. Ask your own advisers about those.
Why a practice’s card mix is unusual
A practice can sell several things at very different prices. In our made-up example, a copay might be $25. An after-insurance balance might be $150. A crown, a procedure or a payment plan installment might run into the hundreds or thousands. The same flat percentage lands differently on each.
That is why the headline rate is the wrong number to compare. Two practices that both pay “2.9% + 30 cents” can have very different effective rates. A practice with mostly $25 copays pays a larger share of each sale to the 30 cent part. A practice that mostly bills larger balances pays more dollars to the percentage part. The way to see it is to split your month into groups and price each one.
The prices, as read on the processors’ own pages
Every price below is taken from the processor’s own page as we read it on November 13, 2026. Prices change and accounts can have custom terms, so check each page and your own account for today’s price.
Stripe’s pricing page
- 2.9% + 30 cents per successful domestic card transaction.
- Invoicing: 0.4% per paid invoice. The page lists no other invoicing plan.
- An extra 0.5% for manually entered cards.
- Disputes: $15.00 for each dispute received and $15.00 for each dispute you respond to manually (refunded for won disputes). $15.00 for each dispute appealed (not refunded).
Square’s fees page
- Tap, dip or swipe: 2.6% + 15 cents.
- Online or invoices: 3.3% + 30 cents.
- Manual entry or card on file: 3.5% + 15 cents.
Notice that a Stripe invoice (2.9% + 0.4% + 30 cents) works out to the same 3.3% + 30 cents as a Square online sale or invoice. Our study uses 3.3% + 30 cents as its flat-rate benchmark for invoices for that reason.
A made-up month at a practice (our arithmetic)
This is made-up math to show the method, not a promise about any practice or any account. We invented a month with three kinds of patient payment and priced each one with the Square prices above. We checked every result with a calculator script.
- 400 copays at $25, tapped or dipped in the office. That is $10,000. At 2.6% + 15 cents, each copay costs $0.80, so the group costs $320.00, or 3.2% of the dollars.
- 60 balances at $150, paid by a payment link. That is $9,000. At 3.3% + 30 cents, each costs $5.25, so the group costs $315.00, or 3.5%.
- 10 treatment payments at $800, typed in over the phone. That is $8,000. At 3.5% + 15 cents for manual entry, each costs $28.15, so the group costs $281.50, or 3.52%.
Total: $27,000 collected and $916.50 in card fees, about 3.39%. That is about $11,000 a year at this pace.
Three things stand out. First, the three groups cost nearly the same percentage, but they are very different in count. The copay group is 400 payments and most of the hand work, yet it is cheap per payment. Second, the phone group is only 10 payments and it costs almost as much as the copays. Third, the balances are where a payment link and a different pricing model both come into play.
Here is a small test of the keyed group. If the same ten $800 payments were instead completed by the patient through a payment link, Square’s online price of 3.3% + 30 cents would cost $26.70 each instead of $28.15. That is $14.50 a month for the group, or $174 a year. It is small on its own, and it also saves staff the time of typing numbers.
What the study says about each group
The study is called “The Flat-Rate Tax.” It was written by Allen Kopelman, the CEO of NPS. It is a model built from published rate schedules, not a survey of practices, and NPS sells interchange pass-through pricing. Use it as a reason to ask for a quote, not as proof of your own savings.
- Online and invoice payments. In the model, interchange pass-through costs 19% to 31% less than flat rate across average tickets from $15 to $2,500. In our made-up month, that range applied to the $315.00 of balance fees is about $60 to $98 a month, or about $720 to $1,170 a year. That is our arithmetic on the study’s range, not a promise.
- In person. From our own arithmetic on the study’s listed inputs, pass-through costs about 6.5% less than Square’s 2.6% + 15 cents at a $15 ticket, and about 19% to 25% less from a $40 ticket upward. A $25 copay sits between those two points, so we put no number on it. That is why your own statement matters.
- Where flat rate can win. Very small in-person tickets, around $15 and under, and brand-new businesses with very low volume.
Two more cautions from the study. Interchange varies by card type, and business and commercial cards can cost more, while Level 2 and Level 3 data can lower them. And the debit cap is narrower than many people think: it is 0.05% + 21 cents plus a 1 cent fraud adjustment, and it applies to large-bank debit, not small-bank debit. NPS has a separate post on whether the debit cap applies to small-bank cards. For a plain explanation of the two pricing models, see where Stripe fees actually go.
How to take a card by phone or on file (how-to)
Practices often keep a card for later, or take one over the phone. Here is how the options compare on price. For what you must tell a patient or what you may store, ask your own advisers. This page does not cover it.
- Keyed in by your staff. You type the number into a terminal or a virtual terminal. On Square’s page, manual entry is 3.5% + 15 cents. On Stripe’s page, manually entered cards carry an extra 0.5%. This is the most expensive of the common ways, so keep it for cases with no better option.
- A saved card (card on file). Once a card is saved with the patient’s agreement, later charges can be run without typing it again. Square’s fees page lists card on file at 3.5% + 15 cents. For how Stripe prices a card you saved, read Stripe’s pricing page, because we do not state a figure for it here.
- A payment link the patient completes. You send a link by text or email, and the patient enters their own card on their own phone. Square lists online sales at 3.3% + 30 cents, and Stripe at 2.9% + 30 cents, plus 0.4% if the link is an invoice.
- Bank payments (ACH). ACH is a bank-to-bank payment. NPS offers ACH, so ask about it when you request a quote.
A simple habit helps: ask which of these four each payment came through when you review your month. A statement that lumps them together hides where the cost is.
How to work out your own mix in ten minutes
- Pull three months of card payments. Your processor dashboard or a statement will show them.
- Sort them into groups. In person, link or online, and keyed or on file. Note the count and the dollars in each.
- Find the average in each group. A group averaging $25 behaves differently from one averaging $800.
- Price each group with the rates on your own agreement. Use the processor’s own page for current prices and your own account for any custom terms.
- Compare to your actual fees. If your effective rate is far above what the groups predict, look for monthly, statement, gateway, dispute or instant payout fees.
- Get one written quote and compare line by line. Ask for the markup, monthly fee, gateway fee, any invoice fee, and the contract terms.
Our guide on how to read your merchant statement walks through the lines, and how much you are really paying on Stripe, Square, PayPal or QuickBooks covers the same exercise across providers. If your practice also sends invoices, see cheapest card processing for invoices and payment links, and for a store that took a similar look, what a retail store saves leaving Square.
When staying put is the right call
- Most of your card payments are small copays under about $15. The study says flat rate can win there.
- Your volume is very low or you are brand new.
- Your practice software already handles patient payments well, and the time it saves is worth more than the fee gap.
Switching starts to deserve a look when balances and treatment payments are a real share of your dollars, when staff type in many cards, or when your yearly fees are a number you notice.
Questions to ask any processor before you move
- What is the markup over interchange, in writing, and is it fixed?
- What do keyed-in and card-on-file payments cost?
- Is there a fee for sending a payment link or an invoice?
- What are the dispute fees, and are they refunded if I win?
- Are there monthly, gateway or statement fees?
- Can I see a sample statement that shows each fee on its own line?
If an answer is “it depends,” ask on what. A clear answer lets you do the arithmetic above yourself.
You can also run your own patient payment numbers through our savings calculator.
Who wrote this, and where NPS fits
Nationwide Payment Systems (NPS) publishes this guide. We are a payments company based in Fort Lauderdale, Florida, in business since 2001, and we sell merchant accounts and invoicing software, so we are not neutral. We offer interchange-plus pricing, ACH, a payment gateway and Smart Invoicing, and we also offer flat-rate options. We do not publish a price list. The study we cite was written by our CEO. NPS offers a free statement review. Browse more in our payments guides, or read the full comparison in cheapest payment processing in 2026.
This page is about card fees. It is not advice about HIPAA or any other medical, privacy, card network or legal rule, and we do not say what any of them requires. Ask your own advisers about those.
We are not the right fit for every practice. If most of your payments are very small copays, or your current setup already costs you little, a simpler arrangement may serve you better.
Bottom line
The cheapest card setup for a practice follows its mix of payments. Small in-person copays, balances paid by link and larger typed-in treatment payments each carry a different price, and the keyed-in group tends to be the costliest per dollar. Pull your own three months, price each group with the processor’s own current page, and compare one written quote line by line. If you would like a second opinion, you can contact our team.
Frequently asked questions
What is the cheapest way for a medical or dental practice to take cards?
It depends on the mix. Small copays taken in person, balances paid online or by payment link, and larger treatment payments typed in by phone each carry different fees. Add up your own month by payment type, then compare quotes line by line. In the study’s model, interchange pass-through costs 19% to 31% less than flat rate for online and invoice sales across $15 to $2,500 tickets. It is a model from a company that sells pass-through, so test it on your own statement.
What do Stripe and Square charge for a patient balance sent as a payment link?
As read on Square’s fees page on November 13, 2026, online sales or invoices are 3.3% + 30 cents. As read on Stripe’s pricing page the same day, 2.9% + 30 cents per successful domestic card transaction, and Invoicing adds 0.4% per paid invoice. Both pages can change, so check them for today’s price.
Does it cost more to type in a patient’s card number?
On Stripe’s pricing page, as read on November 13, 2026, manually entered cards carry an extra 0.5%. On Square’s fees page, as read the same day, manual entry or card on file is 3.5% + 15 cents, against 2.6% + 15 cents for tap, dip or swipe. A payment link the patient completes themselves is priced as an online payment instead.
Is flat rate ever the better choice for a practice?
Possibly. The study says flat rate can still win for very small in-person tickets, around $15 and under, and for brand-new businesses with very low volume. If most of your card payments are tiny copays, run the numbers before switching anything.
How much could a practice save in a year?
Our made-up month has $9,000 a month in balances paid by payment link. In the study’s model, 19% to 31% less on those would be about $720 to $1,170 a year. That is made-up math to show the method, not a promise. Your card mix and fees decide the real number.
Does this page cover HIPAA or other medical rules?
No. This page is only about card fees. It does not say what any medical, privacy, card network or legal rule requires. Ask your own advisers about those.
Does NPS review my current statement for free?
Yes. NPS offers a free statement review.
