The routine therapies for relapsing-remitting multiple sclerosis (RRMS) are common disease-modifying medications, yet are not effective in all patients. The aim of the present clinical trial was to evaluate the therapeutic effects of rapamycin on the clinical and radiological aspects, regulatory T cells proliferation and FOXP3 and GARP gene expression in the patients with RRMS. In this study, eight patients with RRMS were chosen and included in the trial. Patients received rapamycin (Rapacan, Biocon, India) for six months. Magnetic resonance imaging (MRI) of the patients’ brain was taken before and after the therapy. Patients’ expanded disability status scale (EDSS), and FoxP3 and GARP gene expression, and Treg cell proliferation were also been evaluated. All the patients had some degrees of significant reduction in mean plaque area size (P = 0.012, Z = −2.520), and minimum and maximum size of the plaques (P = 0.012, Z = −2.521). EDSS of 50% of patients was decreased after the treatment, yet it was not significant (P = 0.059, Z = −1.89). The expression rate of FOXP3 (P = 0.003) and GARP genes in Tregs increased after the therapy. We found a promising response to rapamycin among our cases with minor side effects and it may be considered as a therapeutic option of this disease.