The upper side of my big toe hurts when i run?

Tight shoes: It sounds like your shoes may be too tight in the depth where your toe is hitting the top of the shoes when it bends.

May be structural: If this is the only time it bothers you, it may be secondary to foot structure or function. I would recommend going to a good running store and looking for a good motion control shoe and try an over-the-counter support, antiinflammatories and rest until comfortable. Have it evaluated by your podiatrist if persists. Dr l.