This study aimed to identify functional microRNAs (miRNAs) and their respective targets as central regulatory factors of tooth movement during orthodontic treatment. Gingival crevicular fluid (GCF) of 24 adolescent patients (< 18 years) treated with a full-mouth multibracket appliance (MBA; Thermal Copper Nickel Titanium archwire) was analyzed for miRNAs-21, -29b, -34a, -126, -132, -146a, and -221. GCF samples were taken from the second premolar in either jaw using non-invasive sampling before, 7 days, 5 weeks, and 3 months after application of orthodontic force (8 samples per patient). Validated miRNA targets and regulated pathways were identified using the miRTarBase database (release 9.0) and Reactome (version 87). All analyzed miRNAs were consistently detected in the GCF (Ct value < 35) and a moderate to high correlation was found between samples taken from the mandible and maxilla before treatment (r = 0.42 to 0.71, all p ≤ 0.041). All miRNAs showed changes in their expression levels with orthodontic tooth movement compared to baseline (significant time effect, all p < 0.001). The general profile indicated an increase in miRNA expression in both jaws with time except for miR-21, which showed reduced levels one week after MBA application (p = 0.046). For miR-34, a significant interaction effect was observed (time × jaw, p = 0.0396) in that lower levels were found after five weeks and three months of treatment in the mandible compared to the maxilla. The medium to late treatment phase was characterized by an increase in miR-146 and miR-221. Gene signaling pathway analysis suggested regulation of cellular response to stress including hypoxia, matrix reorganization and vascular remodeling. Since the identified miRNA profile was linked to targets involved in the remodeling process of the alveolar supporting apparatus and alveolar bone, GCF-derived miRNAs may represent diagnostic biomarkers to monitor cellular processes during orthodontic tooth movement and potentially optimize individual treatment outcomes.