Why does the top of my foot hurt after running?

Tendinitis. There are a couple of major tendons that run across the top of our feet, that can become strained fromo running. Ice, stretch and take an over the counter anti-inflammatory medication if you can.
Stress fracture. If you are a frequent runner you may have sustained a stress fracture. This can easily be found on a plain xray. If the xray is normal you may have developed a neuroma in your foot. This is a benign growth on one of the nerves in your foot. This is usually a clinical diagnosis (test negative) and is treated with cortisone injections. The best treatment is to rest a few weeks and see if improves.