M.T.
Find a good podiatrist. My son had the same complaint and we discovered that he had flat feet (no arches). The doctor said that this was causing stress to his growth plates (which was were the pain was coming from).
The doctor made inserts for him to wear in his shoes and also suggested certain shoes that would provide better support. The doctor also said that if it's caught early enough while the feet are still growing, the inserts can help the feet develop better arches.
He's been wearing them for about 6 months and is doing great.