The present study aimed to investigate the protective effects of Polycan, a β-glucan from Aureobasidium pullulans SM-2001, in a rat model of ovariectomy-induced osteoporosis. Ovariectomized (OVX) rats were orally administered 31.25, 62.5 or 125 mg/kg/day Polycan for 126 days, and alterations in body weight, bone mineral content, bone mineral density, failure load, histological profiles and histomorphometric indices were analyzed. In particular, serum levels of osteocalcin, bone-specific alkaline phosphatase (bALP), calcium and phosphorus, and the urine deoxypyridinoline/creatinine ratio, were measured. Furthermore, the femur, tibia and lumbar vertebrae were harvested from all rats, and histomorphometrical analyses were conducted in order to assess the mass and structure of the bones, and the rates of bone resorption and formation. One group of rats was treated with alendronate, which served as the reference drug. The results of the present study suggested that Polycan treatment was able to inhibit ovariectomy-induced alterations in bone resorption and turnover in a dose-dependent manner. In addition, the serum expression levels of bALP and all histomorphometrical indices for bone formation were markedly increased in the Polycan-treated groups. These results indicated that Polycan was able to preserve bone mass and strength, and increase the rate of bone formation in OVX rats; thus suggesting that Polycan may be considered a potential effective anti-osteoporosis agent.