New York State Medicaid Coverage Policy and Billing Guidance for the 2023-2024 COVID-19 Vaccines

  • Guidance is also available in Portable Document Format (PDF)

Reminder: Pharmacy Provider Options Available for the COVID-19 and Influenza 2023-2024 Vaccine Season

NY Medicaid has posted COVID-19 vaccine billing guidance for this season and is available here. The NY Medicaid Pharmacists as Immunizers Fact Sheet has information on how to bill for vaccines for over and under 19 years of age and a link to the Vaccine for Children (VFC) Program is found here. Please be advised that NY Medicaid does reimburse for the COVID-19 vaccine and administration at NY Medicaid qualified pharmacies for adults 19 years of age and older. Children under the age of 19 are vaccinated for COVID- 19 and all other ACIP recommended vaccines at VFC enrolled providers, including their practitioner’s office, public health clinics or, in most areas their county health department. At this time, pharmacies dually enrolled in NY Medicaid and VFC may also immunize children between the ages of 3 to under 19 years of age for COVID-19, and ages of 2 to under 19 years for influenza, in accordance with the federal PREP Act and/or State law.

Please be advised of the following options when your pharmacy has a request to vaccinate a child under the age of 19:

VFC enrolled pharmaciesmust ensure their pharmacy has ordered adequate VFC stock, and

  • Submit a claim to Medicaid for the administration fee and the VFC eligible vaccination at zero cost.

Non-VFC enrolled pharmaciescan determine how their pharmacy will handle VFC eligible vaccination requests and either:

  • Submit a claim to Medicaid for the administration fee and for the vaccine at zero cost, thereby accepting reimbursement for the administration only as payment in full.
  • Refer member/parent/guardian to obtain the requested vaccination at a VFC provider, such as their practitioner’s office, public health clinic, county health department, or a NY Medicaid and VFC enrolled pharmacy.

There is no out-of-pocket cost for vaccination. It is inappropriate for pharmacies to suggest to the member/parent/guardian to pay out of pocket for VFC covered services.


  • NY Medicaid does not reimburse for out-of-pocket costs to members/parents/guardians for services that are either Medicaid or VFC covered services.
  • If appropriate, multiple vaccines may be administered on the same day and submitted to NY Medicaid according to the links provided above. See Getting a Flu Vaccine and a COVID-19 Vaccine at the Same Time | CDC
  • New York State County Health Department contact information can be found here.
  • Pharmacies may call eMedNY for billing assistance at 800-343-9000.
  • Questions regarding this communication may be directed to