New York State Medicaid Coverage Policy and Billing Guidance for the Administration of COVID-19 Vaccines

Updates as of 2-6-2022 are highlighted in yellow

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

This guidance sets forth New York State (NYS) Medicaid's reimbursement policy for the administration of COVID-19 vaccines approved by the Food & Drug Administration (FDA) or authorized for emergency use and instructions for School Based Health Centers (SBHCs) to bill for the administration of authorized COVID-19 vaccines. Information about vaccines receiving an Emergency Use Authorization (EUA) by the FDA can be found on the FDA's COVID-19 Vaccines web page.

NYS Medicaid's policy for the administration of COVID-19 vaccine will continue to remain in effect in accordance with the Public Readiness and Emergency Preparedness Act (PREP Act). As additional COVID-19 vaccines become available under an EUA, or are otherwise approved by the FDA, this billing guidance will be updated as needed.

NYS Medicaid Coverage & Reimbursement Policy for Administration of FDA Authorized COVID-19 Vaccines

  • The NYS Medicaid program will reimburse NYS Medicaid enrolled and qualified SBHC providers for the administration of COVID-19 vaccines that have been issued an EUA by the FDA for the prevention of COVID-19.
  • Reimbursement for administration of COVID-19 vaccines may be based on a patient-specific order or non-patient specific order ("standing order"). These orders must be kept on file by the provider. Standing orders enable assessment and vaccination of the patient without the need for clinician examination or a patient-specific order from the attending provider at the time of the patient interaction. For more information, please see:
  • The ordering provider's National Provider Identifier (NPI) is required on the Medicaid claim. Ordering providers are required to be enrolled in the NYS Medicaid program.
  • In accordance with federal guidelines, providers are prohibited from charging a co-payment or cost sharing responsibility to Medicaid members for COVID-19 related services. SBHC providers are reminded that Medicaid members under 21 are exempt from all co-payments or cost sharing responsibilities for COVID-19 or non-COVID-19 related services.
  • Providers must not bill NYS Medicaid for the administration of the COVID-19 vaccine to members who are also enrolled in Medicare. Dually eligible enrollees will continue to access full coverage of immunization services through Medicare
  • Payment will not be made to NYS Medicaid providers for the cost of COVID-19 vaccine because the vaccine is available at no cost to providers. Providers must not bill the Current Procedural Terminology (CPT) code for the vaccine.
  • In order to obtain COVID-19 vaccine at no cost, Medicaid enrolled providers must be legally authorized to administer the vaccine and also enroll as COVID-19 vaccine providers with the Centers for Disease Control and Prevention (CDC), the NYS Department of Health Bureau of Immunization, or the NYC Department of Health and Mental Hygiene (NYCDOHMH) Bureau of Immunization. Such providers are considered qualified providers by the Medicaid program for the purpose of COVID-19 vaccine administration.
  • For information on how to enroll in the NYS COVID-19 Vaccination Program and how to register for the NYSIIS or CIR, please visit COVID-19 Vaccine Information for Providers.

    Note that this program is distinct from the Vaccines for Children (VFC) Program and separate enrollment is required.

Billing Instructions and Fees

SBHCs may bill NYS Medicaid for the administration of FDA authorized COVID-19 vaccines when administered by a qualified SBHC provider to Medicaid members.

  • COVID-19 vaccine administration must be billed to NYS Medicaid separately from other SBHC services. SBHCs providing clinic services in addition to and beyond the scope of the COVID-19 vaccine administration service can bill an appropriate Ambulatory Patient Group (APG) claim for the non-COVID-19 vaccine related services provided.
  • SBHC may bill for COVID-19 vaccine administration as stand-alone service when other services are not provided.
  • SBHC administering a COVID-19 vaccine to Medicaid members with Family Planning only coverage should bill a separate claim for COVID-19 vaccine administration using the appropriate rate code representing the COVID-19 vaccine administered from the table below with ICD-10 diagnosis code Z23 (encounter for immunization) as the primary diagnosis on the claim.

SBHC have been assigned the following rate codes to bill for COVID-19 vaccine administration:

SBHC Rate Code Rate Code Description Rate Effective for Dates of
service on or after:
5522 SBHC-PFIZER COVID VACCINE DOSE 1 - 0001A $40.00 4/1/2021
5523 SBHC-PFIZER COVID VACCINE DOSE 2 - 0002A $40.00 4/1/2021
5527 SBHC-PFIZER COVID VACCINE DOSE 3 - 0003A $40.00 8/12/2021
5534 SBHC-PFIZER VACCINE BOOSTER 0004A $40.00 9/22/2021 through 8/30/2022
5524 SBHC-MODERNA COVID VACCINE DOSE 1 - 0011A $40.00 4/1/2021
5525 SBHC-MODERNA COVID VACCINE DOSE 2 - 0012A $40.00 4/1/2021
5528 SBHC-MODERNA COVID VACCINE DOSE 3 - 0013A $40.00 8/12/2021
5526 SBHC-JANSSEN COVID-19 VACCINE - 0031A $40.00 4/1/2021
5529 SBHC-JANSSEN COVID-19 BOOSTER DOSE 0034A $40.00 10/20/2021
5530 SBHC-PFIZER COVID VAC (TRS-SUC) DOSE 1 0051A $40.00 1/3/2022
5531 SBHC-PFIZER COVID VAC (TRS-SUC) DOSE 2 0052A $40.00 1/3/2022
5532 SBHC-PFIZER COVID VAC (TRS-SUC) DOSE 3 0053A $40.00 1/3/2022
5533 SBHC-PFIZER COVID VAC (TRS-SUC) BOOSTER 0054A $40.00 1/3/2022 through 8/30/2022
5535 SBHC-MODERNA VACCINE BOOSTER 0064A $40.00 10/20/2021 through 8/30/2022
5536 SBHC-PFIZER COVID VAC ADMIN AGE 5-11 DOSE 1 0071A $40.00 11/3/2021
5537 SBHC-PFIZER COVID VAC ADMIN AGE 5-11 DOSE 2 0072A $40.00 11/3/2021
5541 SBHC-PFIZER COVID VAC ADMIN AGE 5-11 DOSE 3 0073A $40.00 1/3/2022
5543 SBHC-PFIZER COVID VAC ADMIN AGE 5-11 Booster 0074A $40.00 5/17/2022 to 10/12/2022
5561 SBHC PFIZER C-19 ADM (6MOS-4YRS) 1ST DOSE 0081A $40.00 6/17/2022
5562 SBHC PFIZER C-19 ADM (6MOS-4YRS) 2ND DOSE 0082A $40.00 6/17/2022
5563 SBHC PFIZER C-19 ADM (6MOS-4YRS) 3RD DOSE 0083A $40.00 6/17/2022
5573 SBHC Moderna C-19 ADM (6yrs-11yrs) 1st dose 0091A $40.00 6/17/2022
5574 SBHC Moderna C-19 ADM (6yrs-11yrs) 2nd dose 0092A $40.00 6/17/2022
5575 SBHC Moderna C-19 ADM (6yrs-11yrs) 3rd dose 0093A $40.00 6/17/2022
6119 SBHC - MODERNA VACCINE BOOSTER - 0094A $40.00 3/29/2022 through 8/30/2022
5564* SBHC MODERNA C-19 ADM (6MOS-5YRS) 1ST DOSE 0111A $40.00 6/17/2022
5565* SBHC MODERNA C-19 ADM (6MOS-5YRS) 2nd DOSE 0112A $40.00 6/17/2022
5572 SBHC MODERNA C-19 ADM (6MOS-5YRS) 3rd DOSE 0113A $40.00 6/17/2022
5576 SBHC NOVAVAX C-19 ADM (18 & over) 1st dose 0041A $40.00 7/13/2022
5577 SBHC NOVAVAX C-19 ADM (18 & over) 2nd dose 0042A $40.00 7/13/2022
5587 SBHC NOVAVAX C-19 ADM (18 & over) - Booster Dose 0044A $40.00 10/19/2022
5580 SBHC Pfizer-BioNTech - ADM SARSCOV2 - Bivalent - 30MCG/0.3ML - Booster Dose - 0124A $40.00 8/31/2022
5581 SBHC Moderna - ADM SARSCOV2 - Bivalent - 50MCG/0.5ML - Booster Dose - 0134A $40.00 8/31/2022
5585 SBHC Pfizer-BioNTech - ADM SARSCOV2 - Bivalent - 10MCG/0.2ML - Booster Dose (5 - 11 yrs) - 0154A $40.00 10/12/2022
5586 SBHC Moderna - ADM SARSCOV2 - Bivalent - 25MCG/0.25 ML - Booster Dose (6 - 11yrs) - 0144A $40.00 10/12/2022
5590 SBHC Moderna - ADM SARSCOV2 - Bivalent - 10MCG/0.2ML - Booster Dose (6mos - 5yrs) - 0164A $40.00 12/8/2022
5591 SBHC Pfizer-BioNTech - ADM SARSCOV2 - Bivalent - 3MCG/0.2ML - 3rd Dose (6mos - 4yrs) - 0173A $40.00 12/8/2022

NOTE: Each COVID-19 vaccine administration rate code above represents a distinct COVID-19 vaccine administration CPT code. Providers are required to use the appropriate rate code for the COVID-19 vaccine dose administered. The above rate codes include the actual work of administering the vaccine, including all necessary counseling provided to patients and/or caregivers for the dose administered, required vaccination reporting, and updating of electronic records.

*Rate Code activation letters were sent to SBHC rate-based providers for rate codes 5564 and 5565 with inaccurate descriptions identifying incorrect age parameters for these COVID-19 vaccine administration rate codes. The correct descriptions for rate codes 5564 and 5565 are listed in the above table.

COVID-19 Vaccine Counseling

Effective December 1, 2021, New York State (NYS) Medicaid fee-for-service (FFS) provides reimbursement for COVID-19 vaccination counseling to Medicaid members to encourage the administration of the COVID-19 vaccine. SBHCs must follow the updated policy guidelines outlined in the Updated Coverage Criteria for COVID-19 Vaccine Counseling to bill the below rate code for this service.

SBHC have been assigned the following rate code to bill for COVID-19 vaccine counseling:

SBHC Rate Code Rate Code Description Rate Effective for Dates
of service on or after:

Additional Information:


  • NYS Medicaid Fee-for-Service claim questions should be directed to the eMedNY Call Center at (800) 343-9000.
  • NYS Medicaid Fee-for-Service coverage and policy questions should be directed to the Office of Health Insurance Programs (OHIP) Division of Program Development and Management (DPDM) by phone at (518) 473-2160 or by email at