Running isn't necessarily a pain free exercise and as much as 75% of athletes could possibly get an injury every year. More frequently that not this exercise related injury is not really enough to stop them exercising and they generally just have to back away a little and make use of some minimal treatments to let it get better. In some cases the overuse injury is significant enough that this makes the runner to give up on the sport. There are lots of injuries that can affect runners, impacting on many different areas of the lower limb. Among the most prevalent injuries is what has become known non-technically as top of foot pain or ToFP. Medically this is whats called dorsal interosseous compression syndrome. This is an injury that produces pain on top of the foot, typically around the highest area of the arch of the foot. This generally occurs in barefoot runners as well as athletes who usually forefoot strike instead of rearfoot strike initially whenever they are running. Running using this method will probably try and push the front foot upwards on the rearfoot causing the jamming of the bones of the top of the foot, causing the pain in that location.
At first this is treated with ice to handle the swelling and maybe anti-inflammatory medications to settle it down. Most runners will have to reduce their weekly distances run to also help settle it down. The ideal way to address this is to use 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 is not easy to undertake, which is often avoided to begin with to try and deal with the problem without doing that. In the event the other strategies don't work, then a change in the running technique is most likely suggested.