Background: The study aimed to clinically estimate an influence of a 635 nm diode laser on the stability of orthodontic mini-implants, to assess mini-implants loss, and to evaluate a pain level after the treatment. Materials and Methods: The randomized clinical split-mouth trial included 20 subjects (13 women and 7 men; age: 32.5 ± 6.1 years), 40 implants (RMO, West Colfax Ave., Denver, CO, USA) with a diameter 1.4 mm and length of 10 mm. Mini-implants were placed in the area of the attached gingiva between the second premolar and first molar teeth, 2 mm below the mucogingival junction of both sides of the maxilla. Each implant on the right side (G1, n = 20) of the maxilla was irradiated with a diode laser, and the implants on the opposite side (left, G2, n = 20) were a control group (without laser irradiation). The 635-nm laser parameters; dose: 10 J per point (20 J/cm2), time: 100 s per point, two points (irradiation on a buccal, and a palatal side of the alveolus/implant), the total energy per session 20 J. Laser application protocol: immediately and 3, 6, 9, 12, 15, and 30 days after surgery. The total energy after all therapeutic sessions was 140 J. The implants’ stability was measured employing a Periotest device (Periotest Test Value—PTV) immediately and 3, 6, 9, 12, 15, 30, and 60 days after the insertion of the mini-implants. Results: We found significantly higher secondary stability, lower mean PTV (6.18 ± 5.30) and (1.51 ± 2.25), for self-drilling mini-implants (G1, test group) in contrast to the control, G2 group (9.17 ± 8.25) and (5.00 ± 3.24), after 30 (p = 0.0003) and 60 days (p = 0.0000). Moreover, the analysis of the mini-implants stability after 635-nm diode laser application revealed significant higher stability in comparison with none irradiated implants (G2 group) after 3 days. (p = 0.0000) There was no significant difference in pain level measured on the NRS-11 scale on both sides of the maxilla. (p = 0.3665) An important finding was that all inserted mini-implants survived during a two-month observation period. Conclusions: 635-nm diode laser at laser irradiation increases the secondary stability of orthodontic mini-implants.