What would be causing the clicking in the top/inside of my left foot when i run/walk. it is extremely painful and i'm unable to flex my foot when i walk.

Podiatrist: Clicking can be due to deformed joint motions or slipping of tendons around joints. I recommend that you see a podiatrist for diagnosis and treatment as ignoring persisting symptoms can result in more problems, limping and chronic malfunction. Proper footwear and/or orthotics may be advised after evaluation.

Overuse syndrome: Could be many things. Does the type of shoe make a difference? Did you have an injury? Could be plantar fasciitis or other overuse or inflammatory syndrome. Could also be a small fracture. Best to let your doctor look at it.

Stop running.: Clicking, severe pain and inability to move something are all bad symptoms when it comes to the mid-foot. I strongly recommend that you be evaluated by a foot specialist to minimize further problems. This should be sooner than later.