Since the pain comes only after rigorous exercise, please check your foot wear. May be the foot wear rubs against this portion of the foot. Other possibility is flat foot. It could also be the beginning of arthritis. You may have suffered hairline fracture of any one of the small bones of foot in the area that is painful. It could also be a corn or callus.
Please consult your doctor, preferably a podiatrist. Meanwhile after any exercise, dip feet in warm water. Gently massage your feet with a massage cream or oil. Check your foot wear. Take care!
The medical advice given should not be considered a substitute for medical care provided by a doctor who can examine you. The advice may not be completely correct for you as the doctor cannot examine you and does not know your complete medical history. Hence this reply to your post should only be considered as a guiding line and you must consult your doctor at the earliest for your medical problem.