Running exercise is an effective therapy for the prevention of osteoporosis; however, appropriate duration of exercise has not been determined. We therefore investigated the effect of exercise duration on bone mineral density (BMD) and systemic bone metabolism using young growing rats. Fifteen 8-week-old female Wistar rats were divided into three groups according to running load: control group (no running), short duration (30 min/day) and long duration (180 min/day), and animals ran on a treadmill 5 days per week over an 8-week period. BMD of the tibia was measured using peripheral quantitative computed tomography, and serum levels of tartarate-resistant acid phosphatase (TRAP), a bone resorption marker and alkaline phosphatase (ALP), a bone formation marker were measured to know whether the treadmill exercise would affect systemic bone metabolism. Short-duration running exercise (30 min/day) caused a significant increase in BMD of the metaphyseal trabecula (p < 0.05) with a reduction of serum TRAP levels (p < 0.01) and an increase in serum levels of calcium (p < 0.05) and phosphorus (p < 0.01). Conversely, long-duration exercise (180 min/day) significantly reduced BMD of the diaphyseal and metaphyseal cortex and that of the diaphyseal trabecula with a significant reduction of serum ALP levels and a significant increase in serum phosphorus. These findings suggest that short-duration exercise may increase BMD through suppression of bone resorption, whereas long-duration exercise may reduce BMD through suppression of bone formation. Exercising for short duration but not prolonged exercise is recommended to increase BMD of loaded long bones.