Running is not necessarily a pain free exercise and up to 75% of runners could possibly get an injury every year. More often that not that injury is not really sufficient to stop them training and they usually just need to back off a bit and make use of some minimal treatments to let it get better. In some cases the exercise related injury is significant enough that it forces the runner to discontinue on the running. There are various injuries which could happen to runners, affecting numerous parts of the lower limb. One of the more prevalent injuries is what has become called non-technically as top of foot pain or ToFP. Clinically this is called dorsal interosseous compression syndrome. This is an overuse injury which causes pain on the top of the foot, usually around the top area of the arch of the foot. This generally occurs in barefoot runners as well as athletes who tend to forefoot strike rather then heel strike initially when they are running. Running in this way has a tendency to try and drive the ball of the foot upwards on the rearfoot bringing about the jamming of the bones of the top of the foot, causing the pain in that region.
At first this is managed with ice to deal with the inflammation and maybe anti-inflammatory drugs to settle it down. The majority of runners will need to scale back on their weekly mileage to also help settle it down. The best way to deal with this is to work with more of a heel strike when running and make use of foot orthotics to maintain the rearfoot up so the jamming in the midfoot doesn't occur. While the change in running method could very well be a good way to help this, it's difficult to accomplish, which is generally avoided in the beginning to try and address the problem without doing that. When the other strategies don't work, then a change in the running method is probably recommended.