This study shows that both singular (5 Gy) and fractional (10 Gy) total body irradiation in C57BL/6J mice cause delayed cognitive and motor deficits, with the fractional dose leading to irreversible damage. The mechanisms involve DNA damage-induced oxidative stress and apoptosis, downregulation of BDNF and Tau in the brain, and increased osteoclast activity with reduced RUNX2, sclerostin, and β-catenin in bone. The fractional 10 Gy model provides a stable platform for studying multi-organ radiation injury and testing anti-radiation therapies.