How Michigan Pharmacies Bill Medicaid for Flu Vaccines (in the 2026 to 2027 Flu Season)

If you're a pharmacist in Michigan, you already know that pharmacists are a trusted source for flu shots. Roughly 80% of Michigan residents who got vaccinated in 2021 did so at a pharmacy, according to the Michigan Senate Fiscal Agency's bill analysis of Senate Bill 219 (SB 219) of 2023.

A relatively new addition to the landscape is that Michigan pharmacists can bill Michigan Medicaid directly for flu vaccines if they enrol as a Medicaid provider through CHAMPS, Michigan's Medicaid claims system. This authority is fairly recent: SB 219 was signed in 2023 and allows properly trained Michigan pharmacists to order and administer vaccines to patients age 3 and up without the direction of a physician.

In this blog, we're going to break down how Michigan pharmacies can bill Medicaid for flu vaccines to help you understand the process before you build a billing workflow around it.

What is Senate Bill 219 (SB 219) and what does it mean for pharmacist-provided flu vaccines?

Before SB 219, pharmacists' ability to independently provide certain vaccines was supported by temporary authority tied to the COVID-19 public health emergency.

SB 219 became Public Act 97 of 2023, effective July 19, 2023. This permanently expanded Michigan pharmacists' authority to provide certain vaccines and testing services. After completing the required training, their new authority allows pharmacists to order and administer a qualified immunizing agent (recommended by the Advisory Committee on Immunization Practices (ACIP) and approved or authorized by the FDA) to patients aged 3+ without the direction of a physician.

This law also allows appropriately trained pharmacists to independently order and administer certain FDA-waived tests for flu, COVID and other respiratory infections. For flu or COVID, a pharmacist can dispense an antiviral without a prescription when they determine treatment is needed based on the test result and the other requirements are met.

Enrolling in CHAMPS and billing Michigan Medicaid

CHAMPS, the Community Health Automated Medicaid Processing System, is Michigan Medicaid's online provider enrollment system.

To bill for flu vaccine administration, both the pharmacy and the pharmacist providing vaccination service need to meet Medicaid enrollment requirements. Pharmacists who order and administer vaccines must enroll individually through CHAMPS, using their Type 1 NPI and the applicable pharmacist specialty and subspecialty. The enrollment must be approved in order to be reimbursed. It's best to enroll as early as you can with CHAMPS, as there isn't a standard processing time.

Once the immunization service is administered to the patient, the pharmacy then submits immunization claims. How you submit the billing claim depends on the patient's coverage. Most Michigan Medicaid members receive their coverage through a Medicaid Health Plan rather than traditional fee-for-service Medicaid, so pharmacies should first identify the patient's plan and follow its billing requirements. For fee-for-service members, pharmacies follow MDHHS's pharmacy billing process through its contracted PBA.

A few Michigan Medicaid billing basics:

• Flu vaccine claims are exempt from member copayments, members are not charged.
• A dispensing fee is not paid on seasonal flu vaccine claims. Instead, pharmacies bill the applicable vaccine administration fee using the required NCPDP claim fields.
• For members enrolled in a Medicaid Health Plan, the plan must cover at least the pharmacist services included in Michigan Medicaid policy, but pharmacies should still confirm the plan's specific billing, prior authorization, documentation, enrollment, credentialing and contracting requirements before submitting a claim.

Pharmacists must log every immunization in the Michigan Care Improvement Registry, and for eligible patients under 19, pharmacists are required to share information about the Vaccines for Children (VFC) program and follow VFC vaccine billing rules.

As with any clinical services, it's important to keep your records up-to-date and audit-ready. MDHHS requires pharmacies to maintain documentation supporting Medicaid-reimbursed services, including a way to identify the pharmacist who ordered or administered the vaccine and documentation showing compliance with applicable training, reporting and scope-of-practice requirements. Claims that don't meet these requirements could be denied or recouped after payment.

Bill Michigan Medicaid cleanly this season

MedMe can help you get your CHAMPS-enrolled pharmacy ready before the flu rush.

Codes and MDHHS policy

MDHHS communicates Medicaid coverage, coding, and billing changes through policy bulletins, which are then incorporated into the online Medicaid Provider Manual through quarterly updates. Before each flu season, be sure to check it out for the most up-to-date information.

For pharmacy claims, it's also important to check the current MDHHS Pharmacy Benefits Administrator claims processing guidance for the NCPDP fields, vaccine product requirements, and administration fee billing instructions that apply to seasonal flu vaccines, because reimbursement amounts and billing requirements can change.

A note on Vaccines For Children (VFC)

For pediatric patients under 19 years old, Michigan's VFC program supplies vaccines at no cost for VFC-eligible patients, including those enrolled in Medicaid. At each vaccination visit, the pharmacist will screen patients for eligibility.

For VFC-supplied vaccines, the vaccine product itself is provided at no cost and therefore isn't reimbursed by Medicaid; the administration fee is billed separately.

A simple way to build this into your flu-season workflow is to screen for and document VFC eligibility during intake for every patient under 19, alongside your standard consent and clinical screening. Identifying potential VFC eligibility before the vaccination helps ensure the correct vaccine supply and billing pathway are used from the start. If your pharmacy does not participate in VFC, Michigan Medicaid requires you to inform potentially eligible patients or caregivers about VFC and provide information on local participating providers, unless another payer covers the vaccine cost.

Common issues

• Enrollment gaps. CHAMPS enrollment is separate from state licensure. Before flu season, confirm that both the pharmacy and each pharmacist providing Medicaid vaccination services have the required active Medicaid enrollment, subspecialty designation, and training documentation.
• MHP coverage checks. For Medicaid Health Plan members, don't assume the fee-for-service billing workflow applies. MHPs must cover the pharmacist services included in Michigan Medicaid policy, but each plan may have different billing, credentialing, documentation, prior authorization and contracting requirements.
• Stale bulletins. Don't rely on last season's billing guide. Check the current Medicaid Provider Manual, supplemental policy bulletins and applicable pharmacy claims-processing guidance for current coverage, coding and reimbursement requirements.
• Skipping the registry log. Don't treat Michigan Care Improvement Registry (MCIR) reporting as part of the claim itself. Michigan law separately requires pharmacists to follow MCIR reporting requirements; for pharmacist-administered qualified vaccines given to patients age 20 or older, SB 219 specifically requires reporting within 72 hours. Build registry reporting into the vaccination workflow rather than trying to reconcile records later.
• Missing the VFC step. Medicaid patients under 19 require special attention to Vaccines for Children eligibility. Michigan Medicaid requires pharmacies to address potential VFC eligibility, and vaccination services for this population are subject to VFC coordination. If you serve pediatric patients, screen for VFC eligibility before selecting vaccine inventory or starting the billing workflow.

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