The aim of this study was to evaluate the effect of photobiomodulation therapy (PBMT) with the association of red and infra-red laser therapy in the healing of the post-extraction sockets of third lower molars. Twenty patients were submitted to extraction of lower third molars and the post-extraction sockets were treated using two different approaches in a randomized split-mouth design: The test side received the PBMT with red (λ 660nm) and infra-red laser therapy (λ 808nm) and the control side was not irradiated. The PBMT was applied immediately and 3 and 7days after the surgical procedure. Post-extraction socket healing was assessed by the bone repair score, bone density, and fractal dimension analysis 7 and 90days after the surgical procedure, using cone-beam computed tomography images. Additionally, clinical analyses were performed 3, 7, 14, 30, and 90days after the surgical procedure, considering the occurrence of pain, edema, and bleeding, as well as the quality of the oral mucosa repair, assessed using a visual analogue scale. The clinical analysis showed that PBMT reduced edema and improved the repair of oral mucosa at 7days after surgery, while the tomographic analysis showed no significant differences between groups. Dual-wavelength PBMT improved the post-operative clinical course in patients undergoing lower third molar extraction, without altering bone repair.