© 2021, Springer Medizin Verlag GmbH, ein Teil von Springer Nature.Purpose: We aimed to evaluate and compare effects of photobiomodulation (PBM) and low-magnitude high-frequency mechanical vibration (HFMV) on orthodontic retention. Methods: Sixty-four female Wistar albino rats were divided into 9 groups (2 negative and positive controls each, 3 PBM and 2 HFMV groups) and studied for 25 days. In the experimental groups, closed nickel–titanium closed coil springs with a 50 cN force were placed for 10 days between the maxillary incisor and molar. PBM and HFMV were applied daily over long- (15 days) and short-term (7 days) retention periods. The PBM groups received PBM with a single wavelength (650 nm) or higher wavelengths (532, 650, 940 nm) for 9 min per day. HFMV groups received HFMV of 10, 20, and 30 Hz for 10 min per day. Right and left maxilla were assessed using micro-computed tomography imaging and real-time polymerase chain reaction. The amount of tooth movement during the retention period, expression levels of cyclooxygenase‑2 (COX-2), osteoprotegerin (OPG), and receptor activator of nuclear factor-kappa B ligand (RANKL) mRNA gene expression levels, OPG/RANKL ratios, alveolar bone trabecular thickness (Tb.Th), trabecular number (Tb.N), and structure model index were analyzed. Kruskal–Wallis and Mann–Whitney U tests were used for multiple comparisons of the nonparametric distributed data and binary comparisons, respectively. Results: When using the long-term retention protocol, PBM and HFMV treatment increased Tb.N (p < 0.05) and decreased COX‑2 mRNA gene expression levels (p < 0.05) and Tb.Th (p < 0.05) compared to controls. For short-term retention, PBM and HFMV decreased the amount of relapse tooth movement compared to controls. In addition, Tb.Th (p < 0.05) and the mRNA gene expression levels of COX‑2 and RANKL (p < 0.05) were decreased. Conclusion: PBM and HFMV might be able to support retention after orthodontic tooth movement by reducing bone resorption and increasing bone quality.