Running isn't actually a pain free exercise and up to 75% of runners can get an injury every year. More frequently that not that injury isn't enough to prevent them exercising and they typically just need to back off a bit and make use of some small interventions to let it heal up. Occasionally the injury is serious enough that it forces the athlete to discontinue on the running. There are many different injuries that could affect runners, affecting many different areas of the lower limb. Among the more prevalent injuries is what has become called non-technically as “top of foot pain” or ToFP. Clinically this is what's called dorsal interosseous compression syndrome. This is an injury which causes pain on the top of the foot, commonly around the top area of the arch of the foot. This generally occurs in barefoot runners and runners who are inclined to forefoot strike rather than rearfoot strike first whenever they are running. Running this way has a tendency to try and drive the forefoot upwards on the rearfoot creating the jamming of the bones of the top of the foot, bringing about the pain in that area.
At first this top of foot pain is managed with ice to handle the swelling and maybe anti-inflammatory medicines to settle it down. Most runners will have to reduce their weekly mileage to also help settle it down. The simplest way to treat this is to use more of a heel strike when running and use foot supports to maintain the arch up so the jamming in the midfoot does not occur. While the alteration of running form could possibly be an effective way to help this, it's not easy to perform, which is frequently avoided at first to try and treat the issue without doing that. When the other approaches are unsuccessful, then a change in the running method is probably indicated.