The aim of this study was to evaluate in a cohort of patients with peri-implant mucositis: (a) the efficacy of professional mechanical debridement therapy assisted using Bioptron Hyperlight Therapy on the reduction in periodontal indexes and (b) the reduction in total oxidative salivary stress. Forty subjects with a diagnosis of peri-implant mucositis were enrolled and randomly assigned to the Study Group (mechanical debridement therapy assisted using Bioptron Hyperlight Therapy) or Control Group (mechanical debridement therapy alone). The study duration was 6 months. Data on plaque index (PI), bleeding on probing (BoP), probing pocket depth (PPD), and pain relief on Visual Analogue Scale (VAS) were recorded at T0, T1 (14 days), T2 (1 month), and T3 (6 months). Group differences were assessed using Student’s t-test and Pearson’s Chi-squared test of homogeneity. PI and PPD decreased in the Study Group at the [T0; T1] time interval and during the overall time of observation significantly more than in the Control Group; BoP and pain on VAS decreased significantly faster in the Study Group than in the Control Group. Differences in Salivary Antioxidant Test (SAT) changes were not significant at any time interval. Patients’ gender and smoking habit were not correlated with the clinical outcomes. Clinical parameters related to peri-implant mucositis significantly improved in the Study Group, which demonstrated the clinical efficacy of the Bioptron Hyperlight Therapy as an adjunct to standard of care for the treatment of peri-implant mucositis. The RCT was registered at the US National Institutes of Health #NCT05307445.