I have pain at the top of my foot after running.

Sprain?: If you can continue to weight bear without much pain, the chances are it is a simple foot. You can try simple Rest, Ice, Compression and Elevation measures. If you find that you are not able to put weight on it at any stage, see a Dr. You may need an X Ray to rule out a stress fracture

Extensor tendonitis : You may have runners extensor tendonitis, a simple test of this is to push your toes up against your hand and see if this replicates the pain. If so then you need to rest and consider lacing your shoes in a different manner (Lydiard lacing for example). If rest and changing your lacing does not work see a physiotherapist or your GP.

Agony of defeet.: To a doctor who specializes in foot problems, the top of the foot is an awfully big place. It is filled with many a structure that can cause the symptoms you are having. To remove doubt, it is best to have your foot evaluated by a specialist, preferably one who runs.

Stress fracture?: If you do a lot of running/walking or if you have recently increased that amount you are doing a stress fracture is a possible cause. These show up as very subtle swellings on the long bones of your foot - they improve with adequate rest. I would recommend you rest for 7-10 days to allow it to settle and if it is still very sore you could get an x-ray at that stage.