Talk to General Physician on Flat Feet Issue

I love to stay fit and for this I really work hard. I have good stamina but my running and sprinting is greatly hindered by my lower legs. I the beginning of the running session it feels normal but with time muscles in my lower legs they start to hurt. If I continue doing it for a month or so then I really have to take a break for a week or so as the pain gets more and more. I run on softer tracks and wear proper jogging shoes but still I face this issue. With my stamina I go 10Km in one session but the leg pains limits it to 3 or 4km. Is there anything that could be done in this regard?

Thank you.