The aim of the present study was to evaluate the effects of LLLT prior to muscle injury with and without post-injury irradiation on the expression of isoforms of myosin heavy chain (MyHC), calcineurin (CaN), and myostatin during the repair process. Wistar rats were divided into five groups: control (n = 7); injury (n = 21); LLLT + injury (n = 21); injury + LLLT (n = 21), and LLLT + injury + LLLT (n = 21). Cryoinjury was performed on the tibialis anterior (TA) muscle. The injured groups were euthanized at 3, 7, and 14 days after injury. LLLT was performed using an infrared laser (780 nm) with the following parameters: 10 J/cm, 40 mW, 10 s per point, 8 points, and 3.2 J of total energy. At the end of each period, the TA muscle was removed for the analysis of MyHC, CaN, and myostatin gene expression using real-time PCR. The data were tested statistically by Kruskal-Wallis with Dunn's post hoc test (p < 0.05). The results demonstrated that prior irradiation reduced the mRNA expression of all proteins at 3 days. Post irradiation reduced the mRNA expression of MyHC-1, MyHC-2a, MyHC-2b, and CaN at 7 days. Prior irradiation combined with post-injury irradiation reduced the mRNA expression of MyHC-2x and CaN at 14 days and increased the mRNA expression of myostatin in the same period. In conclusion, different protocols of photobiomodulation can modulate the expression of the different isoforms of MyHC, CaN, and myostatin during the repair process. It is noteworthy that the combination of the prior and post-injury irradiation was the protocol that most promoted changes in the final phase of the repair process.