How does the flu vaccination work? the flu vaccine works by making you sick with the flu so that you won’t get the flu later. the flu vaccine is a dose of antibodies that fight the flu virus. the flu vaccine is injected under the skin in an inactive form and the immune system responds with antibodies to the flu protecting you from future exposure to the flu. the flu vaccine is injected under the skin and the endocrine system responds by sending hormones to fight the virus.