After receiving a flu shot, a small portion of people complain of pain in their upper arm/shoulder that lasts for several weeks or months. A theory of why this occurs suggests that the vaccine is being injected into the joint capsule or bursa and causing an inflammatory response.
For relief, you can apply a heating pad to the shoulder/upper arm and rest the arm. If after several days your pain still persists, you should contact your physician that provided you the flu shot. At that point, your physician might refer you for physical therapy.
Physical therapy treatment is usually brief and can provide pain relief and increased range of motion. With use of manual techniques such as massage and stretching, range of motion can be restored and pain decreased. Strengthening exercises can help to restore any weakness that has occurred from lack of use of the arm.
If you have experienced pain from a flu shot that is lasting longer that you expected, seeing a physical therapist can help facilitate healing of your muscles, tendons and shoulder joint.