This article explains how to bill Medicare Part B for influenza and COVID-19 vaccines using MedMe, from confirming the patient's coverage and running an insurance eligibility check, through claim submission, to handling denials and re-submitting through the pharmacy (drug) benefit when needed.
Table of Contents
Overview
Flu and COVID-19 vaccines for Medicare patients are covered under Medicare Part B, the medical benefit, not the pharmacy benefit you may be used to billing through your pharmacy management system. These claims are submitted as professional medical claims (the same CMS-1500/837P format used by physician offices), and MedMe handles that submission for you.
The good news for your patients: Medicare Part B covers flu and COVID-19 vaccines at $0 out of pocket. There is no coinsurance, no copay, and the Part B deductible does not apply, as long as the claim is billed correctly and your pharmacy accepts assignment (MedMe claims are submitted with assignment accepted).
Please Note: This article covers Original Medicare (Part B) billing. Patients with a Medicare Advantage plan (Part C) follow a different path — see Step 1 and When to Use the Drug Benefit Instead below.
Which vaccines belong to which Medicare benefit?
Not every vaccine is a Part B vaccine. Getting this right up front prevents most vaccine claim denials.
Benefit | Vaccines | How it's billed |
Part B (medical), preventive | Influenza (seasonal), COVID-19, pneumococcal, hepatitis B (for intermediate/high-risk patients) | Medical claim through MedMe |
Part B (medical), treatment | Vaccines needed to treat an injury or direct exposure, e.g. tetanus after a wound, rabies after an animal bite | Medical claim, billed with the injury/exposure diagnosis (not Z23) |
Part D (drug) | All other adult vaccines — shingles (Shingrix), RSV, Tdap boosters, hepatitis A, and anything else ACIP-recommended for prevention | Pharmacy benefit through your pharmacy management system (PBM/NCPDP claim) |
Reminder: Part D vaccines that are ACIP-recommended are also $0 out of pocket for patients with Part D coverage, but they must go through the pharmacy benefit, not a medical claim. A Part D vaccine billed to Part B will be denied.
How Medicare Covers Flu and COVID-19 Vaccines
Influenza: Medicare covers one flu vaccine per flu season (additional doses are covered when medically necessary). "Per season" is not "per calendar year": a patient vaccinated in October 2026 and again in September 2027 has received one vaccine in each of two seasons, and both are covered.
COVID-19: Medicare covers COVID-19 vaccines and additional doses in line with current FDA/CDC recommendations, with no seasonal once-per-year restriction comparable to flu.
Diagnosis code: Both use ICD-10 code Z23 (Encounter for immunization). Your MedMe billing template pre-fills this.
Part B vaccine code reference
Your MedMe billing template will present the right options. This table is a complete reference for all Part B preventive vaccines, useful when reading claims and remittances.
Vaccine | Product code(s) | Administration code | Coverage notes |
Influenza (seasonal) | 90616 (mFluSiva, mRNA trivalent), 90653 (Fluad), 90656, 90657, 90658 (Fluzone), 90660 (FluMist), 90661 (Flucelvax), 90662 (Fluzone High-Dose), 90673 (Flublok) — 2026-27 season | G0008 | Once per flu season; more if medically necessary |
COVID-19 | 91319/91320 (Comirnaty), 91321/91322 (Spikevax), 91323 (mNexspike), 91304 (Nuvaxovid) — check the current CMS list as 2026-27 formulation codes are released | 90480 | Per current FDA/CDC recommendations; no once-per-season limit |
Pneumococcal | 90671 (PCV15, Vaxneuvance), 90677 (PCV20, Prevnar 20), 90684 (PCV21, Capvaxive), 90732 (PPSV23, Pneumovax 23), 90670 (PCV13, legacy) | G0009 | One PCV dose for patients who haven't been vaccinated; if PCV15 is given, PPSV23 follows one year or more later; patients who completed PCV13 + PPSV23 may get PCV20/PCV21 five years or more after the last dose |
Hepatitis B | 90739 (Heplisav-B), 90746 (Engerix-B / Recombivax HB), 90743, 90744, 90740/90747 (dialysis formulations) | G0010 | Covered only for intermediate/high-risk patients (e.g. ESRD/dialysis, diabetes, hemophilia); the claim must include the ordering physician's name and NPI |
Home administration add-on (any of the above given in the patient's home) | — | M0201 | Paid in place of/alongside the standard admin fee per CMS rules |
Diagnosis for all preventive vaccine encounters | Z23 | — | Treatment vaccines (tetanus/rabies after injury or exposure) instead use the injury/exposure diagnosis |
📌 Tip: MedMe bills your vaccine claims against the local Medicare fee rate; no need to look up or set pricing yourself. All four preventive vaccine families are $0 to the patient: no coinsurance, no deductible.
Reminder, same-day flu + COVID: When a patient receives a COVID-19 vaccine and a flu (or other Part B) vaccine on the same day, Medicare requires modifier 59 on the second administration code (e.g. 90480 and G0008-59). Without it, one of the administration lines may be denied. MedMe billing templates for co-administration handle this; if you are entering codes manually, don't forget the modifier.
Before You Bill: Pharmacy Requirements
Your pharmacy must be set up for Medicare Part B billing before the first claim goes out. These are completed during your MedMe Medical Billing onboarding:
Medicare enrollment (PECOS) for the pharmacy, with an active PTAN, including a Mass Immunizer PTAN if your pharmacy enrolled as a mass immunizer for vaccine billing.
NPIs on file: the pharmacy's Type 2 NPI and the Type 1 NPI for each pharmacist who will administer vaccines.
EDI enrollment with your Medicare Administrative Contractor (MAC). MedMe completes this on your behalf during onboarding, establishing the electronic connection used to submit your claims.
Please Note: If you're not sure your Medicare setup is complete, check with your MedMe Account Manager before administering with the intent to bill. Claims submitted before enrollment is effective are denied and often cannot be recovered.
Step 1: Patient Intake, What to Collect and Ask
Most vaccine claim problems are created at intake. Two minutes of verification here prevents weeks of denial follow-up later.
MedMe collects insurance at patient intake by default. When a patient books through your MedMe scheduling link (or completes walk-in intake), they are prompted to enter their medical insurance, and it is saved to their patient profile automatically; for most patients, no manual entry is needed. Pharmacy staff should still review the insurance on the patient profile for completeness and accuracy, since patients frequently enter their pharmacy card where their medical plan should be.
Pharmacy staff can also add or update insurance directly on the patient profile. When an insurance card image is uploaded, MedMe runs OCR on the card to select the right payer and pre-populate the insurance details; upload a clear photo of the card, then verify the pre-filled fields.
Verify at the counter:
The patient's medical insurance card(s). For Medicare patients this is one of: the red, white, and blue Original Medicare card showing the patient's Medicare Beneficiary Identifier (MBI), which is what you need for a Part B claim, or a Medicare Advantage plan card (UnitedHealthcare, Humana, Aetna, etc.). If the patient has Medicare Advantage, the claim goes to that plan, not to Original Medicare.
The patient's pharmacy benefit card as well (BIN / PCN / Group / Member ID). MedMe doesn't store drug-benefit details, so add them to the patient's profile in your pharmacy management system; that's your fallback path if the medical claim can't be completed (see PBM re-submission below).
Demographics exactly as they appear with Medicare: full legal name spelling, date of birth, and address. Mismatches are a leading cause of failed eligibility checks and rejected claims.
Ask:
"Do you have Original Medicare, or is your Medicare through a private plan like Humana or UnitedHealthcare?" Many patients say "I have Medicare" when they are enrolled in a Medicare Advantage plan. Always confirm with the card.
"Do you have any other insurance — a supplement, retiree coverage, or coverage through a spouse?" This determines whether a secondary payer exists.
"Have you already had a flu shot this season?" A second same-season flu vaccine without medical necessity will be denied as a duplicate/frequency issue.
"When was your last COVID-19 vaccine?" Confirm the patient is due per current recommendations.
Reminder: For Part B claims, the payer on file must be the patient's medical coverage, not a drug plan (e.g. OptumRx, Caremark, Express Scripts). If the profile shows a PBM as the medical insurance, correct it before running eligibility.
Step 2: Run the Insurance Eligibility Check
Once insurance is on the patient profile, run an eligibility check from the profile before (or at) the visit. MedMe sends a real-time eligibility inquiry to the payer and returns the response in seconds to a couple of minutes.
Open the patient profile and locate the insurance card on the left-hand side.
Select the arrow to run insurance verification.
Review the response in the pop-up modal: subscriber info at the top, benefit details under Service Types.
What to look for on a Medicare eligibility response:
Coverage status, Active. Confirms the patient's Part B coverage is active for the date of service.
Entered-in-error. The details sent didn't match the payer's records — usually a wrong MBI, wrong payer selection, or a name/DOB mismatch. Correct the profile and re-run.
Deductible / coinsurance amounts. For flu and COVID-19 vaccines these do not apply; the patient owes $0 regardless of deductible status, so there is normally no patient payment to collect for these services.
Please Note: A missing or failed eligibility response does not always mean the patient is uninsured; some payers only return eligibility to enrolled/in-network NPIs. If the patient presents a valid Medicare card and the details are verified, you can proceed and let the claim adjudicate.
For a full walkthrough of the eligibility feature, see How to Check Insurance Eligibility in MedMe.
Step 3: Document the Encounter and Complete the Billing Questionnaire
After administering the vaccine, complete the encounter documentation as usual, then the billing questionnaire — the final questionnaire in Edit Documentation for Medical Billing-enabled appointment types.
Confirm the CPT codes. Your flu or COVID-19 billing template pre-selects the recommended codes: the vaccine product code plus the administration code (G0008 for flu, 90480 for COVID-19). Verify the product code matches the vaccine actually administered.
Co-administration? If flu and COVID-19 were given at the same visit, ensure modifier 59 appears on the second administration code (e.g. G0008-59).
Confirm the ICD code. Z23 applies to vaccine encounters and is paired with each CPT line.
Units. Administration codes and standard vaccine products are 1 unit.
Enter the Rendering Provider: the name and NPI of the pharmacist who administered the vaccine.
Check the confirmation box confirming encounter details, coding, and insurance are complete, then select Complete.
MedMe validates the claim, submits it electronically to your MAC, and tracks it from there.
Warning: Billing fields cannot be modified after the confirmation box is checked and the questionnaire is saved, because the claim is transmitted for submission. If you spot an error after saving, contact MedMe Support through the chat widget.
For a walkthrough of medical billing end-to-end — insurance verification, encounter documentation, and completing the billing template — see How to Start Medical Billing with MedMe.
Step 4: Track Your Claim
Track claim progress in your Claims Viewer / Billing Dashboard:
Acceptance by the clearinghouse/payer is the first status you'll see on a claim.
Medicare adjudication typically completes in about 14 days; payment follows by direct deposit shortly after the remittance is issued.
Each claim shows its status (Submitted, Accepted, Rejected, Paid, Denied) along with payer reason codes when a claim isn't paid in full.
If you don't have dashboard access, contact your Account Manager. See How to Use the Claims Viewer with MedMe for a full walkthrough.
Handling Denials and Rejections
Vaccine claims are among the cleanest claims in medical billing; most denials trace back to a small set of causes. When a claim is denied, the remittance includes a CARC (reason) code.
What you see | What it usually means | What to do |
CO-109, Not covered by this payer/contractor | Patient is enrolled in a Medicare Advantage plan, so Original Medicare has no jurisdiction | Re-run eligibility, update the patient profile to the MA plan and resubmit to it, or re-bill through the pharmacy benefit (see next section). Do not appeal to Medicare; it can't pay a claim it has no jurisdiction over |
Patient not found / ID mismatch (rejection) | MBI, name spelling, or DOB doesn't match Medicare's records | Verify against the Medicare card, correct the profile, resubmit |
CO-18, Duplicate | Same vaccine already billed for this patient (e.g. second flu shot this season, or the claim was submitted twice) | Confirm with the patient/records; if it's a true duplicate, no action; if medically necessary, contact Support to review |
Administration line denied when flu + COVID same day | Missing modifier 59 on the second administration code | Add the modifier and resubmit the corrected claim |
CO-16, Missing/incomplete information | A required field (NPI, POS, etc.) was missing or invalid | Review the remark codes, correct, resubmit |
Vaccine not covered under Part B | A Part D vaccine (e.g. Shingrix, RSV, Tdap) was billed as a medical claim | Re-bill through the pharmacy benefit, see next section |
Denied and rejected claims can generally be corrected and resubmitted. Medicare's timely filing limit is 12 months from the date of service, so act on denials promptly. If a denial reason isn't clear, contact MedMe Support through the chat widget; our billing team reviews the remittance detail and advises on the fix.
When to Use the Drug Benefit Instead (PBM Re-Submission)
Sometimes the medical claim isn't the right path, or fails, and the vaccine should be billed through the patient's pharmacy (drug) benefit instead. This is why we recommend collecting the patient's drug benefit card (BIN / PCN / Group / Member ID) at intake and adding it to their profile in your pharmacy management system, even for a Part B vaccine; MedMe doesn't store drug-benefit details.
When this applies:
The patient has a Medicare Advantage plan (MA-PD). Many MA-PD plans process flu and COVID-19 vaccines administered at a pharmacy through the pharmacy benefit at the point of sale. If your Part B claim denied CO-109 and your pharmacy isn't contracted with the patient's MA plan for medical claims, running the vaccine through the plan's PBM in your pharmacy management system is usually the fastest way to get paid.
The vaccine is a Part D vaccine. Shingles, RSV, Tdap, and most other adult vaccines are never Part B for prevention; they belong on an NCPDP claim to the patient's Part D plan. Patients pay $0 for ACIP-recommended vaccines under Part D.
Your Medicare Part B enrollment isn't active yet and the patient has drug coverage that will pay — a stop-gap while enrollment completes.
How to re-submit through the PBM:
Pharmacy-benefit (NCPDP) claims are adjudicated in real time through your pharmacy management system, not through MedMe. To re-submit:
Retrieve the patient's drug benefit details (BIN / PCN / Group / Member ID) from their pharmacy card or their profile in your pharmacy management system.
Process the vaccine claim in your pharmacy management system as you would a dispensing claim, using the vaccine's NDC and your system's vaccine-administration workflow.
The PBM adjudicates in seconds and returns the patient copay (typically $0 for ACIP-recommended vaccines under Part D and most MA-PD plans).
Reminder: Never bill both the medical claim and the pharmacy claim for the same vaccine. If a denied medical claim is later re-billed to the PBM (or vice versa), make sure the original claim is not resubmitted or is reversed, to avoid duplicate billing.
Troubleshooting and FAQ
The eligibility check returns "entered-in-error." The submitted details don't match the payer's records. Verify the MBI (11 characters, letters and numbers, no spaces or dashes), exact name spelling, and DOB against the Medicare card, then re-run.
The patient says they have Medicare but their card is from Humana / UnitedHealthcare / Aetna. That's a Medicare Advantage plan. Bill that plan (if your pharmacy is set up for it) or process the vaccine through the plan's pharmacy benefit in your pharmacy management system; do not submit to Original Medicare.
Can I charge the patient if I'm unsure the claim will pay? For flu and COVID-19 vaccines under Part B there is no patient cost-sharing, and MedMe claims are submitted with assignment accepted. If coverage itself is in doubt, resolve eligibility first rather than collecting payment for these vaccines.
Does the patient need a prescription? No prescription is required for Medicare Part B flu or COVID-19 vaccination, and no physician order or referring provider is needed on the claim.
We ran an off-site flu clinic, anything different? Yes: the service location on the claim matters (it determines claim routing and place of service). Let your Account Manager know before billing for off-site or employer-clinic events so your setup is configured correctly.
The billing questionnaire isn't appearing. The appointment type may not be Medical Billing enabled; contact your Account Manager.
Conclusion
Billing flu and COVID-19 vaccines to Medicare Part B in MedMe comes down to four habits: confirm the patient truly has Original Medicare (card + eligibility check), collect the drug benefit card as a fallback, let the billing template drive the coding (Z23, G0008 / 90480, modifier 59 for same-day co-administration), and act on denials quickly — routing Medicare Advantage and Part D situations through the pharmacy benefit instead. Patients pay nothing for these vaccines when billed correctly.
For additional help, contact MedMe Support through the chat widget or reach out to your Account Manager.
References: CMS Vaccine Pricing · CMS Flu Shot Provider Resources · Medicare Part B Immunization Billing (MLN006799) · Medicare Part D Vaccines (MLN908764)