Isoflurane is a commonly used inhalational anesthetic, clinically and in animal experimental studies. Although it has been reported as safe, recent findings suggest that despite widespread use, isoflurane‐induced inhalational anesthesia can lead to various pathophysiological and cognitive alterations. Therefore, we aimed to investigate the long‐term behavioral and white matter consequences of repeated isoflurane exposure. Twenty 3‐month‐old C57BL/6J male mice received one exposure of isoflurane for 40 min or 2 exposures to isoflurane separated by 3 days. Behavioral paradigms (open field, balance beam, foot fault, rotarod, elevated zero maze, tail suspension, water maze, and social recognition tests) were administered at 1, 3, 5, 7, and 90 days post exposure. Animals exposed to repeated isoflurane showed significant motor deficits on the balance beam and increased anxiety‐like behavior. Animals exposed to single isoflurane showed impaired performance on the foot fault test. Diffusion tensor imaging showed that repeated isoflurane exposure led to long‐term disruption of water diffusivity in corpus callosum (CC) white matter. Furthermore, 2‐D structure‐tensor analysis from stained brain sections showed differences in the microstructural organization of CC white matter in mice with single versus repeated isoflurane exposures. These results suggest that behavioral deficits observed up to 90 days after repeated isoflurane exposure resulted from, at least in part, altered CC white matter microstructural integrity.