This case discusses a six-year-old girl who presented with a two-month history of bloody diarrhea, abdominal pain, anorexia, and weight loss. After the failure of conventional treatment for inflammatory bowel disease (IBD), gastrointestinal basidiobolomycosis, a rare fungal infection caused by *Basidiobolus ranarum*, was considered. She was transitioned to antifungal treatment with itraconazole, which led to significant improvement. The case highlights the importance of distinguishing this rare infection from other inflammatory conditions to avoid misdiagnosis and inappropriate treatment.