BK virus infection is most often associated with urologic disease in patients who have undergone renal or bone marrow transplantation. We report a rare case of biopsy-confirmed BK virus encephalitis in an immunocompromised patient with hemorrhagic cystitis, in whom dramatic imaging findings were present despite relatively mild clinical symptoms. MR imaging demonstrated widespread increased signal intensity on T2- and fluid-attenuated inversion recovery-weighted images, with restricted diffusion, in the cerebellum, cerebral white matter, and deep gray matter structures. The simultaneous presence of urologic abnormalities and neurologic deficits in certain immunocompromised patients should prompt consideration of BK virus encephalitis.