Background Photobiomodulation therapy (PBM), due to its anti-inflammatory, analgesic effects, and most importantly as a non-invasive procedure, has currently gained a special setting in pain relief and the treatment of Spinal cord injuries (SCI). However, the mechanism of action of the PBM is not yet completely understood. Methods In this study, SCI is induced by an aneurysm clip. Adult male rats were divided into 4 groups: Control, SCI, SCI + PBMT 90 seconds, and SCI + PBMT 117 seconds. After 7 weeks, hyperalgesia, allodynia, and functional recovery were assessed. Fibroblasts were counted after H&E staining. The expression of HDAC2, DNMT3a, GAD65, and GFAP after 4 weeks of daily PBMT (90 and 117 s) was probed by western blotting. Results Both PBMTs (90 & 117 seconds) significantly improved the pain and ability to move and fibroblast invasion was reduced. SCI + PBMT 90s, increased GAD65, HDAC2, and DNMT3a expression. However,PBMT 117s decreased GFAP, HDAC2, and DNMT3a. Conclusion PBMT 90 and 117 s improved the pain, and functional recovery equally. Yet, the mechanism of action appears to change with different durations of radiation.