Evidence pointed towards the benefits of Marantodes pumilum in treating osteoporosis after menopause; however, the detailed mechanisms still have not been explored. Therefore, this study aims to identify the molecular mechanisms underlying M. pumilum's bone-protective effect via the involvement of RANK/RANKL/OPG and Wnt/β-catenin signaling pathways. Ovariectomized adult female rats were given M. pumilum leaf aqueous extract (MPLA) (50 and 100 mg/kg/day) and estrogen (positive control) orally for twenty-eight consecutive days. Following the treatment, rats were sacrificed, and femur bones were harvested. Blood was withdrawn for analysis of serum Ca2+, PO43-, and bone alkaline phosphatase (BALP) levels. The bone microarchitectural changes were observed by H&E and PAS staining and distribution and expression of RANK/RANKL/OPG and Wnt3a/β-catenin and its downstream proteins were determined by immunohistochemistry, immunofluorescence, Western blot, and real-time PCR. MPLA treatment increased serum Ca2+ and PO43- levels and reduced serum BALP levels (p bone microarchitecture and the loss of bone glycogen and collagen content were mitigated by MPLA treatment. Levels of RANKL, Traf6, and NF-kB but not RANK in bone were decreased; however, levels of OPG, Wnt3a, LRP-5, Frizzled, Dvl, β-catenin, RUNX, and Bmp-2 in bone were increased following treatment with MPLA. In conclusion, MPLA helps to protect against bone deterioration in estrogen deficiency state and thus, this herb could potentially be used to ameliorate osteoporosis in women after menopause.