The present study evaluated the prebiotic effect of a standardised aqueous extract of Anoectochilus formosanus (SAEAF) and its effects on osteoporosis in ovariectomised (OVX) rats. The OVX rats were randomly divided into five groups and orally treated with water, SAEAF (200 and 400 mg/kg daily) and inulin (400 mg/kg daily) for 12 weeks. The sham group was orally treated with water. The SAEAF treatment enhanced the number of faecal bifidobacteria in OVX rats. The results of a Ca-balance experiment showed that SAEAF increased apparent Ca absorption and retention. The OVX rats were killed after SAEAF treatment lasting 12 weeks. The SAEAF decreased the caecal pH values and increased the caecal wall weight, caecal mucosa calbindin-D9k mRNA expression, free-Ca concentration and levels of SCFA in the caecum. The mineral content, density and biomechanical strength of bones were lower in OVX rats than the sham group, but these bone losses were prevented by SAEAF administration. Microtomography scanning showed that the SAEAF-treated rats had higher trabecular bone volume than the OVX rats. These results suggest that SAEAF prevented bone loss associated with ovarian hormone deficiency in the rats.