Sometimes people who receive the flu shot feel flu-like symptoms. This can be for a number of reasons. The most common is that your body is doing what it should be doing. It is recognizing the flu virus and developing antibodies to fight future infections. Another possible reason is that in the 2 weeks that it takes the flu shot to be effective, you may be infected with the flu virus or you could be infected with other illnesses, like the common cold that also produce flu-like symptoms. Lastly, you could be infected by a strain of the flu virus that you are not protected from by getting the flu shot.