Why does my foot muscle ache after running fast?

Over use: Pain can indicate that you need orthotics or a shoe change. I suggest you see a sports podiatrist.

That depends.: There are many muscles in your feet. Four layers of muscles on the bottom or plantar surface of your feet. The pain might be muscle strain or it could be plantar fasciitis, an inflammation of the ligament on the bottom of your foot. Good running shoes and/or arch supports are often helpful.