To identify the best low level laser photobiomodulation application site at the same irradiation time to increase the viability of the skin flap in rats. Eighteen male rats (Rattus norvegicus: var. Albinus, Rodentia Mammalia) were randomly distributed into three groups (n = 6). Group I (GI) was submitted to simulated laser photobiomodulation; group II (GII) was submitted to laser photobiomodulation at three points in the flap cranial base, and group III (GIII) was submitted to laser photobiomodulation at 12 points distributed along the flap. All groups were irradiated with an Indium, Galium, Aluminum, and Phosphorus diode laser (InGaAlP), 660 nm, with 50 mW power, irradiated for a total time of 240 s in continuous emission mode. The treatment started immediately after performing the cranial base random skin flap (10 × 4 cm dimension) and reapplied every 24 h, with a total of five applications. The animals were euthanized after the evaluation of the percentage of necrosis area, and the material was collected for histological analysis on the seventh postoperative day. GII animals presented a statistically significant decrease for the necrosis area when compared to the other groups, and a statistically significant increase in the quantification of collagen when compared to the control. We did not observe a statistical difference between the TGFβ and FGF expression in the different groups evaluated. The application of laser photobiomodulation at three points of the flap cranial base was more effective than at 12 points regarding the reduction of necrosis area.