It is well known that ionizing radiation-induced toxicity to normal tissue has functional consequences in the brain. However, the underlying molecular alterations have yet to be elucidated. We have previously reported cognitive impairments with concomitant changes in dendritic complexity, spine density and inflammation in mice at 6-24 weeks postirradiation. The goal of this study was to determine whether metabolic changes in the mouse hippocampus after whole-body (4 Gy) or cranial (9 Gy) X-ray irradiation might trigger some of the incipient changes contributing to the persisting pathology in the radiation-injured brain. Metabolomic and lipidomic profiling of hippocampal tissue revealed that radiation induced dyslipidemia in mice at two days and two weeks postirradiation. Strikingly, significant changes were also observed in metabolites of the hexosamine biosynthesis pathway, a finding that was further confirmed using orthogonal methodologies. We hypothesize that these changes in hexosamine metabolism could induce endoplasmic reticulum stress and contribute to radiation-induced cognitive impairments. Taken together, our results show that molecular phenotyping is a valuable approach to identify potentially detrimental pathway perturbations that manifest significantly earlier than gross structural and functional changes in the irradiated brain.