top of foot pain. Metatarsal Stress Fracture - Pain in one of the long thin bones that runs along the top of your foot and attaches to your toes. You may notice swelling and some redness and it's very painful to the touch. Usually affects runners and athletes who may have over done it while training. Press along the shaft of the bone toward the outside and then toward the inside and you will feel stabbing pain. See a podiatrist right away for an X-ray. As you can see there are many factors that can contribute to pain in top of foot. Since many conditions affecting the top of foot can worsen if left untreated, visit your podiatrist as soon as possible for correct diagnosis and treatment.