Running is not actually a pain free activity and as much as 75% of athletes can get an injury every year. More frequently that not that exercise related injury is not really sufficient to prevent them exercising and they generally simply have to back away somewhat and make use of some modest interventions to let it get better. At times the exercise related injury is serious enough that this makes the athlete to discontinue on the running. There are various injuries that might happen to runners, impacting many different areas of the lower limb. Among the most prevalent injuries is what has become called non-technically as top of foot pain or ToFP. Medically this is called dorsal interosseous compression syndrome. This is an injury that produces pain on the top of the foot, typically about the top area of the arch of the foot. This commonly occurs in barefoot runners and athletes who usually tend to forefoot strike rather then heel strike initially when they are running. Running in this way will probably try and force the forefoot upwards on the rearfoot which causes the jamming of the bones of the dorsum of the foot, leading to the pain in that place.
Initially top of foot pain it is managed with ice to deal with the inflammation and perhaps anti-inflammatory drugs to settle it down. Nearly all runners will have to reduce their weekly mileage to also help settle it down. The ultimate way to address this is to work with more of a heel strike when running and make use of foot supports to keep the rearfoot up so the jamming in the midfoot does not happen. While the change in running form can be an effective way to help this, it's difficult to try and do, and it is frequently avoided originally to try and deal with the issue without doing that. If the other methods fail to work, then a change in the running technique is probably advised.