Medical billing fees make more sense when you price a month of claims from coverage checks through payment. A low submission fee can become several transaction charges, while a higher per-claim price may already include eligibility checks and remittances. Those totals can be much closer than the advertised rates suggest.
For a pharmacy comparing proposals, compare the monthly fees alongside your team's ability to understand and follow its claims. You can estimate transaction charges and staff time before signing. It's harder to know how much revenue better visibility and follow-up could help you collect until you've used the service.
What you're paying for
Clearinghouses charge for transactions such as submitting a claim or requesting eligibility information. Software platforms charge for the tools around that activity and may include transactions in their fees. Outsourced billing companies charge for people to prepare, submit and follow claims, often as a percentage of collections. One proposal can combine all three.
For example, AdvancedMD advertises billing services at 4–8% of collections, depending on practice size, specialty and complexity, with core software included. MedPrecision's pricing includes a quote-specific monthly minimum for its solo-practice offer and passes through certain third-party costs. Both illustrate why the percentage alone is only part of the price.
Establish the unit before comparing rates: a submitted claim, a paid claim and an eligibility request each count differently. For a collections-based fee, establish which receipts enter the calculation. Your medical billing agreement should clearly identify the clinical revenue it covers so you can separate it from dispensing revenue.
If you submit through an intermediary's BIN in your dispensing system, the service may convert that transaction into a medical-benefit claim. Its fees may count dispensing-system submissions and related actions, not only the medical claims it sends to the payer. Ask whether rejected attempts, reversals and resubmissions are billable, and whether those charges sit inside the service fee or alongside it.
Eligibility checks and insurance lookup costs
An eligibility check asks a known payer about a patient's coverage and benefits. Insurance discovery searches for coverage when the pharmacy doesn't have reliable insurance information. A Medicare beneficiary identifier lookup is a separate request. Stedi's eligibility overview distinguishes these tasks, which can have different prices even when a quote calls them all “insurance lookup.”
Medical and prescription coverage also require different inquiries. CMS distinguishes medical X12 270/271 eligibility transactions from pharmacy NCPDP transactions. Finding the Rx information needed to route a prescription doesn't establish the medical benefits available for a clinical service. See medical benefit versus pharmacy benefit for that coverage distinction.
Count checks separately from visits. A pharmacy might check coverage when booking a vaccine appointment and again before the service, or check both primary and secondary coverage. Under per-request pricing, those can be separate charges for one encounter. Also ask what happens when a search finds no coverage or a request fails. Stedi's billing rules, for example, exempt specified technical and payer-availability failures; an inactive-coverage response can still be billable.
How small transaction fees add up
Stedi's posted starting rates, checked in October 2026, are $0.30 per claim submission, $0.30 per medical eligibility check and $0.20 per adjudicated claim delivered through an electronic remittance advice, or ERA. The ERA charge counts claims, so one file containing ten adjudicated claims represents ten billable units.
Consider a hypothetical month with 100 claim submissions, 100 eligibility checks and remittances covering 100 adjudicated claims. The bill is $30 for submissions, $30 for eligibility and $20 for remittances: $80 total, or $0.80 per submitted claim. If the pharmacy checks coverage twice for each claim, the eligibility bill becomes $60 and the total becomes $110, or $1.10 per submitted claim.
Now compare a hypothetical platform fee of $1 per submitted claim that includes those eligibility checks and ERAs. Its usage bill is $100 in either case. Against that bundle, the separate transaction charges are $20 lower with one check per claim and $10 higher with two. The advertised $0.30 submission price and $1 bundle price look much further apart than the resulting bills.
That comparison covers usage. Add each option's subscription and any other billable activity to reach the monthly total. Stedi applies lower rates to later transactions in its monthly volume tiers and passes through certain payer surcharges; the example stays within its starting tiers. Discovery is separately priced, starting at $1.50 per standard search, so include it when the pharmacy needs to find coverage.
What a platform bundle changes
Platforms can pass through clearinghouse charges, mark them up or include them in a broader fee. Stedi describes those pricing models for its platform partners. The pharmacy buys the platform's tools and included usage together, so compare that package with the tools and transaction services you'd otherwise pay for separately.
Ask what happens after the claim is submitted. Does the quoted fee include payer responses, status checks, remittances and help understanding unresolved claims? A submitted claim may still be awaiting payer processing or a payment decision. Seeing a rejection brings follow-up into view and gives your team information to investigate the problem. Compare the fee against both the information you'll receive and the help available to act on it.
DocStation, for example, includes eligibility checks and ERAs without separate transaction charges; its pricing page lists the current fees. When comparing a bundle like that with a per-transaction offer, include all the chargeable requests in the latter's total.
Some bundles include a monthly allowance and charge overages. Check which events consume that allowance, whether locations share it and whether unused volume expires. A busy vaccination month can favor included usage, while a quiet month can leave the pharmacy paying for volume it doesn't use. Run both months through the quote rather than assuming the bundle will always be cheaper.
A lower billing-service percentage can cost more
Suppose two hypothetical outsourced billing quotes cover the same medical collections, software and transaction charges. Quote A charges 5% with a $1,200 monthly minimum. Quote B charges 7% with no minimum.
At $15,000 in monthly collections, A charges $1,200 and B charges $1,050. A's effective rate is 8%, making the advertised 5% offer $150 more expensive. At $30,000, A charges $1,500 and B charges $2,100. For a seasonal vaccination program, calculate each month separately; slow months can trigger minimums that disappear in an annual percentage estimate.
The remaining staff work can change the result again. Suppose A leaves your team 20 hours of billing work each month and B leaves five. At an assumed fully loaded staff cost of $40 an hour, that adds $800 to A and $200 to B. At $30,000 in collections, both cost $2,300 including that work. For staff already on payroll, those hours represent capacity you could use elsewhere; outsourcing them won't necessarily reduce payroll.
Use an actual pharmacy case to test the promised service. If a DME claim needs a missing order, who contacts the ordering practitioner, obtains the record and follows the claim afterward? If a vaccine claim is rejected, who fixes the enrollment or submission problem? A proposal that leaves those calls with your team carries a different staff cost from one that assigns them to the billing service.
Fee terms that change the total
For percentage fees, specify how patient payments, older receivables, refunds and recoupments affect the collection base. The ERA reconciliation guide can help connect claim payments to deposits when reviewing that calculation.
Count bundled software once and include any system you'll retain. Use the pharmacy EHR selection guide to assess the clinical record you'll need alongside billing. Add onboarding, migration and integration charges to the first-year budget.
Price the exit as well: the notice period, any continued fees for collecting outstanding claims and the cost of moving claim and payment records. Ask who will follow unpaid claims after termination and whether the outgoing and incoming services could both charge on those collections.
The value of being able to investigate claims
Prescription claims commonly receive an adjudication response at the point of sale. With a typical medical claim, an immediate submission acknowledgement confirms receipt or acceptance for processing; the payer's decision and remittance follow separately. A workflow that stops at the submission response can leave unpaid claims unnoticed, even when the original claim was prepared correctly. The pharmacy needs a way to receive those later updates, reconcile payments and investigate unresolved claims.
The outsourced-fee example above holds collections constant. Your team's ability to investigate unpaid claims can also affect what the pharmacy collects. You may not discover gaps in your current process until you can see claim histories, read payer responses and get help understanding what needs attention.
Suppose a claim has stayed unpaid after a rejection your team couldn't interpret. With the response and claim history available, the pharmacy can investigate the issue and determine whether a correction is appropriate. Any payment collected through that follow-up belongs in the value comparison alongside the fee and staff time. Before you've used a service, that potential is harder to estimate than a subscription or transaction charge.
A demonstration can show whether your own team can open a claim's history, review the payer's response or remittance and understand the next question to investigate. Also establish who helps when the team reaches something it can't resolve.
