Running can pound your entire body, not just the legs and hips. Some common reasons for shoulder and neck pain from running include fist clenching and tilting the head forward. Both constrict and strain muscles, and can add up over the course of a simple jog. Extraneous movement of the arms, such as too much pumping while running, can also exaggerate motion induce fatigue, and that arm movement translates up to the shoulders and neck. Finally, a simple lack of stretching or hydration can lead to issues, and so can basic stress that creeps up on you.