Malakoplakia is a rare inflammatory condition characterized by impaired macrophages unable to completely digest and kill phagocytized bacteria, resulting in partially digested bacterial components accumulating within the phagolysosome. Malakoplakia typically presents in immunocompromised individuals due to underlying disease or to medication effects and is rarely diagnosed in the pediatric population. The urinary tract is the most commonly involved site, followed by the gastrointestinal (GI) tract, mainly affecting the descending colon, sigmoid colon, and rectum. Treatment focuses on the use of antibiotics that concentrate in macrophages such as quinolones and trimethoprim-sulfamethoxazole as well as cholinergic agents such as bethanechol, which raise intracellular levels of cyclic guanosine monophosphate in macrophages to improve bactericidal activity. We report a rare case of GI tract malakoplakia in a pediatric patient undergoing treatment for leukemia.