Health Central has a nice section on foot pain you might want to check out but you may have to see a doctor, hopefully a podiatrist, to really figure this out. However, a lot of foot pain can be remedied by changing your shoes or by adding appropriate insoles. I was having pretty severe pain on the sides of my feet that was remedied by cutting a slit in the side of my shoes. That obviously won't work in your case but it does indicate that small fixes can be quite helpful at times. You can find some recommendations for home treatment of pain in this section below.