How Medicare covers vaccines depends on the type of vaccine and the reason it is prescribed. Medicare Part B (either through Original Medicare or a Medicare Advantage plan) covers vaccines after you are exposed to a dangerous virus or disease. For example, it will cover tetanus shots after you step on a rusty nail. It also covers three vaccines under the preventive care benefit – flu, pneumonia, and hepatitis B. All other vaccines should be covered by your Part D prescription drug plan. Every Part D plan must have all commercially available vaccines on its list of covered drugs (formulary), but costs may differ.