Fixed appliance (FA) therapy predisposes patients to white spot lesions (WSLs). The F-ACP complex (amorphous calcium phosphate nanoparticles enriched with carbonate and fluorine and coated with citrate) has been effective for in vitro enamel remineralization. The aim of this study was to evaluate the efficacy of the F-ACP complex in remineralizing WSLs after FA therapy. One hundred and six adolescents (aged 12–20 years) were randomized into study and control groups after FA therapy. Patients in the study group were advised to use dental mousse containing F-ACP applied within Essix retainers for six months. The presence of WSLs was recorded at baseline (T0), 3 months (T1), and 6 months (T2) according to the International Caries Detection and Assessment System (ICDAS). Visual Plaque Index (VPI) and Gingival Bleeding Index (GBI) were recorded. Among 106 study participants, 91 (52 and 39 in study and control groups, respectively) completed the study. The results showed that the ICDAS score was significantly lower (p < 0.001) in the study group than in the control group between T0 and T2. The application of mousse containing the F-ACP complex inside Essix retainers for six months is effective in remineralizing white spot lesions in patients after FA therapy without side effects.