Background Pediatric gastrointestinal basidiobolomycosis is an unusual fungal infection caused by Basidiobolus ranarum, an environmental saprophyte found worldwide. Typically, basidiobolomycosis presents as a subcutaneous infection or soft tissue tumor-like lesion, and rarely involves the gastrointestinal tract. Gastrointestinal basidiobolomycosis is most common in young infants. It has no definitive clinical presentation, and almost all cases are misdiagnosed during the initial presentation. Case presentation We report the case of a 4-year-old Saudi boy who presented to the emergency department with abdominal pain, nausea, vomiting, and weight loss. Ultrasonography revealed a target sign. Based on the ultrasonography findings, surgery was performed, which revealed the presence of intussusception. Eventually, the patient was diagnosed with intussusception secondary to intra-abdominal basidiobolomycosis based on the histological findings. The patient was readmitted and intravenous voriconazole therapy was initiated. One week after the second admission, the patient developed abdominal pain, nausea, vomiting, inability to hold down food, and constipation. Computed tomography of the abdomen was suggestive of small bowel obstruction, which was managed conservatively. The patient responded well and was subsequently discharged with a prescription of oral voriconazole. Conclusions This case reveals that gastrointestinal basidiobolomycosis can cause intussusception. This report will inform clinicians of the importance of considering gastrointestinal basidiobolomycosis in the differential diagnosis of chronic abdominal pain in children, even in the absence of fever or a clinically obvious abdominal mass, especially in countries such as Saudi Arabia, where cases have been reported.