Muscle contusion usually results from a direct blunt impact and is frequently associated with contact sports. Muscle contusion results from microscopic muscle fiber and capillary disruption causing a microhemorrhage dissecting torn fibers and remaining viable muscle fibers. Recent studies concluded that some physical methods, including pulsed ultrasound (PU) and pulsed electromagnetic field (PEMF) treatment, accelerate and facilitate wound healing, improve scar quality and have beneficial effects on muscle and tendon healing. However, there are few studies on the effects of the early use of physical methods, such as PU and PEMF, on the expression of neurotrophic factors. The objective of this study was to investigate the effects of the early application of PU and PEMF, measured through the expression of BDNF in the muscles (gastrocnemius) and spinal cords of rats after skeletal muscle contusion. In the spinal cords and muscles, there was a significant increase of BDNF expression in the PEMF and PU groups, a greater increase was found in the PEMF group than in the PU group. In conclusion, PEMF is a useful therapeutic method that improves muscle healing after muscle contusion.