Appendiceal mucinous neoplasm is a rare tumor, found in 0.2%-0.3% of appendectomies. Inflammatory bowel disease (IBD) is a known risk factor for colorectal cancer; however, appendiceal mucinous neoplasm is rarely reported in IBD patients. Here we report a rare case in a patient with Crohn's disease after ileocecal resection. She complained of recurrent, severe right lower quadrant pain. Further investigation revealed stenosis at the terminal ileum with a clear appendiceal orifice on magnetic resonance enterography and colonoscopy. She was referred for surgical evaluation after failure of medical management. The diagnosis of low-grade appendiceal mucinous neoplasm was confirmed by pathology after an uneventful laparoscopic ileocecal resection. Although this tumor is rare in IBD patients, a high index of suspicion is needed in those presenting with disease flare-ups, and pathological examination remains essential for diagnosis. This case underscores the diagnostic challenges and clearly highlights the importance of thorough evaluation.