Best Answer: Hi:)), Registered Nurse here; Sorry to hear your feeling bad. The answer is yes the flu shot can make one sick, and throwing up is certainly seen with the flu.The flue shot stimulates your bodies immune system to kick out antibiotics to increase the resistance of getting the flu. believe if you get the shot while you are sick with some other infection, it could actually make you sicker. Even if you are taking antibiotics, or have taken them less then 2 weeks prior to the shot, it can make you sick.