The present study was designed to characterize the bone protective effects of (−)-epiafzelechin (EAF), a flavan-3-ol, in mature ovariectomized mice model and its ability to stimulate osteoblastic activity and inhibit osteoclastic activity. Mature C57BL/6 mice (three to four months old) were either ovariectomised (OVX) or sham-operated and subjected to treatment (vehicle, 17β-oestradiol (E2, 200 μg/kg/day) or EAF (500 μg/kg/day) orally for six weeks. EAF and E2 significantly reduced urinary calcium (Ca) excretion, serum osteocalcin (OCN), and urinary deoxy-pyridinoline (DPD); increased bone mineral density (BMD); and improved micro-architectural properties in OVX mice. EAF significantly increased cell viability, alkaline phosphatise (ALP) activity, and collagen content, as well as runt-related transcriptional factor 2 (Runx2) mRNA expression in murine osteoblastic MC3T3-E1 cells. In addition, EAF significantly reduced the viability of osteoclast precursor murine leukemia monocyte RAW 264.7 cells and tartrate-resistant acid phosphatase (TRAP) activities in mature osteoclastic RAW 264.7 cells. EAF is a bioactive flavan-3-ol that protects estrogen deficiency-induced bone loss in OVX mice and exerts direct modulating effects in bone cells in vitro.