In preclinical studies, fructooligosaccharide (FOS) showed beneficial skeletal effects but its effect on peak bone mass (PBM) and bone loss caused by estrogen (E2) deficiency has not been studied, and we set out to study these effects in rats. Short-chain (sc)-FOS had no effect on body weight, body composition, and energy metabolism of ovary intact (sham) and ovariectomized (OVX) rats. scFOS did not affect serum and urinary calcium and phosphorus levels, and on calcium absorption, although an increasing trend was noted in the sham group. Sham and OVX rats given scFOS had better skeletal parameters than their respective controls. scFOS treatment resulted in a higher bone anabolic response but had no effect on the catabolic parameters. scFOS increased serum levels of a short-chain fatty acid, butyrate which is known to have osteogenic effect. Our study for the first time demonstrates that in rats scFOS at the human equivalent dose enhances PBM and protects against E2 deficiency-induced bone loss by selective enhancement of new bone formation, and implicates butyrate in this process.