Yes but know that if you have an injury, you risk it taking longer to recover. You do need a boosted circulation to aid your body to repair injuries but if you do any sort of exercise which can create damage (such as high impact exercise like running or jumping...etc). These sorts of exercises cause micro-tears and these microtears on top of already-there-injuries is only going to mean your body will take longer to recover from the initial injury.
When you're finished exercising, make sure you stretch- but not too far, use a foam roller to boost circulation and ice it afterwards. If you can, take a few rest days more then normal, walk by all means but just keep tabs on the running if you want it repaired sooner rather then later.