Pain on the top of the foot in a runner has a limited number of sources. The prior postings touch on of the two most frequent of these sources. A stress fracture is a distinct possibility, especially if there is any associated swelling. If you have associated swelling, get a professional evaluation, including x-rays. On the other hand, the problem may be constriction and pressure on the top of the foot created by the shoe lace system of your running shoes. If there is no associated swelling, then try relacing your shoes, skipping the eyelet or lace ring that places the laces on top of your area of pain. This change in the lacing system should produce a noticable and permanent relief. If not, see a professional for evaluation. In either case, remember that ice is your friend.