Low-level laser therapy (LLLT) could be an alternative for the treatment of swelling and pain after orthognathic surgery, but there is a paucity of data in the literature on the effects of its use. This study verified the efficacy of an LLLT protocol to reduce swelling and pain after orthognathic surgery. Ten healthy patients who underwent a bilateral sagittal split with Le Fort I osteotomy were randomly selected for this study. The LLLT protocol consisted of intraoral and extraoral application to one side of the face after surgery (irradiated side); application to the other side was simulated (non-irradiated side). The irradiated and non-irradiated sides were compared regarding the swelling coefficient and were assessed for pain using a visual analogue scale. There were no significant differences between the irradiated and non-irradiated sides regarding swelling and pain in the immediate postoperative assessment. Swelling decreased significantly on the irradiated side in the postoperative assessments on days 3, 7, 15, and 30. Self-reported pain was less intense on the irradiated side at the 24-h (1.2 vs. 3.4) and 3-day (0.6 vs. 2.1) assessments, but at 7 days after surgery neither side showed pain. This LLLT protocol can improve the tissue response and reduce the pain and swelling resulting from orthognathic surgery.