Malakoplakia is a rare granulomatous disorder characterized by defective phagolysosomal activity in macrophages and the presence of Michaelis-Gutmann (MG) bodies, often affecting immunosuppressed individuals. Although it most frequently involves the genitourinary tract, gastrointestinal involvement - particularly in the rectum and sigmoid colon - has been documented. We report a rare case of rectal malakoplakia in a 28-year-old female with penetrating ileocolonic Crohn's disease (CD) on infliximab. During surveillance colonoscopy, distal rectal mucosal nodularity, erythema, and friability were noted. Histopathology showed foamy histiocytes containing periodic acid Schiff-positive, diastase-resistant MG bodies, and CD68 confirmed histiocytic origin. A diagnosis of rectal malakoplakia was rendered, and the patient was managed with ciprofloxacin while continuing immunosuppressive therapy and a scheduled follow-up colonoscopy. Malakoplakia may mimic malignancy or inflammatory bowel disease clinically and endoscopically, making histologic evaluation essential for accurate diagnosis. Escherichia coli is the most commonly implicated organism, and fluoroquinolones are typically effective treatments. Surgical intervention is generally reserved for refractory cases. This case highlights the need to consider malakoplakia in the differential diagnosis of atypical rectal lesions in immunosuppressed patients, including those with CD, to ensure timely and appropriate management.