How to Work Out When Your Shoulder Hurts After 2nd-Shot COVID Vaccine A U.S. Navy corpsman administers a U.S. Marine with the Pfizer-BioNTech COVID-19 vaccine on Camp Lejeune, North Carolina, January 15, 2021. (Rachel K. Young-Porter/U.S. Marine Corps) If you have had vaccines or flu shots in the past, you may remember the typical soreness many feel in the shoulder area. This COVID shot is no different as they tend to “go in deep” to get the shot into muscle tissue, so you may feel some tenderness. Personally, my second shot was not as bad as I expected it to be, but I kept moving, worked out and was drinking more than a gallon of water a day during the first few days. Some experience more than just tenderness to a point that touching or lying on it while sleeping hurts.