This is a problem that is becoming very common in runners especially with the trend to barefoot or minimalist running (which paradoxically is claimed to reduce the number of injuries ..... NOT, as we are seeing so many now).

The pain is generally use due to the forefoot trying to dorsiflex more on the rearfoot that compresses the joints and bones on the top of the foot. If the bone can not take the load, then the problem develops.

To save me repeating the advice, check the advice given here:
Top of Foot Pain Management in Barefoot Runners

Dorsal Midfoot Interosseous Compression Syndrome