Muscle contusion has a negative effect on muscle function. Although several studies showed that pain control and muscle recovery is facilitated by pulsed electromagnetic fields (PEMF), there has not been much research regarding the specific effects of PEMF on them. The aim of the present study is to investigate effects of PEMF on pain and muscle recovery following extensor digitorum longus (EDL) contusion injury through measuring the expression of the c-fos proto-oncogene and nerve growth factor (NGF). Significantly reduced c-fos expression in the spinal cord was shown in PEMF groups compared with control (CON) groups. There was no significant difference between PEMF1 and CON1, but significantly increased NGF expression was shown in PEMF3 and PEMF5 compared with in CON groups, where the numbers in the group names are the days from contusion. In conclusion, PEMF could be used to not only reduce pain in muscle injuries by down-regulating cfos expression in the spinal cord, but it could also influence muscle healing through increasing NGF expression in the injured muscle.