Purpose: Discomfort, edema, infection, and root sensitivity are common side effects of periodontal surgery. The efficacy of photobiomodulation (PBM) in reducing pain and healing of wounds has been studied earlier. The aim of this research is to assess the efficacy of 1064 nm diode laser in reducing postoperative discomfort and promoting wound healing following periodontal flap surgery. Methods: This split-mouth, double-blind, randomized, controlled clinical trial included 24 patients with bilateral 5–8 mm deep periodontal pockets requiring surgical periodontal therapy. One quadrant was assigned into the laser-treated group, and the other functioned as the sham laser control group. On the day of surgery and subsequently every day until day eight, the amount of discomfort felt at the surgical site was noted. Landry’s wound healing index was used to evaluate healing in the first- and second-weeks after surgery. Results: The experimental sites had significantly lower Wong-Baker FACES pain rating scores than the control sites (p < 0.001). At 1-week, the healing index revealed a statistically significant difference between the experimental sites (83.4%) and control sites (25.0%) in terms of excellent healing, followed by very good healing (66.7%). The experimental group continued to score higher than the control group throughout the second week of the follow-up period, although the differences were not statistically significant. Conclusion: Patients’ reported pain and painkiller usage dramatically decreased following flap surgery using the 1064-nm diode laser. Compared to the control group, majority of patients in the experimental group reported having excellent postsurgical outcomes. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2024.