Recent studies have shown that apigenin not only inhibits bone resorption by osteoclasts but also induces osteoclast apoptosis. However, the influence of apigenin on osteoporosis in animals is relatively unknown. The purpose of this study was to examine the bone-protective effects of apigenin in estrogen-deficient ovariectomized rats. Three-month-old female Sprague-Dawley rats were either sham-operated or ovariectomized and fed AIN-93G diet for 7 weeks to induce bone loss. To confirm bone loss, we used a newly developed non-invasive technique involving zoom-in micro-computed tomography. Apigenin was administered at a dose of 10 mg/kg three times a week for 15 weeks. Our results indicate that apigenin not only increased the mineral content and density of the trabecular bone at the neck of the left femur, but also decreased body weight and dietary consumption. Moreover, our biochemical results indicate that apigenin has a positive effect on bone turnover. The present data suggest that apigenin should be considered for use in the treatment of osteoporosis.