Why do my gums feel odd and throb after i run?

Gingivitis: It sounds like you could have gingivitis or some degree of periodontitis. You should see a dentist for a full exam and diagnosis. The throbbing and odd feeling is due to your increased heart rate and blood pressure from running. The gums are very vascular and the increased blood flow is causing the already irritated gums to throb. Just a theory...Please see your dentist.

They shouldn't: It is not normal to have throbbing gums after you run. It is possible that you have a periodontal (gum) infection. Have your dentist evaluate this right away.