Gastrointestinal basidiobolomycosis (GIB) is a rare fungal infection with few reported cases worldwide. We report here the first case diagnosed in Oman in a previously healthy 5-year-old Omani female child who had been thought initially to have an abdominal malignancy. The case was referred to the Royal Hospital, Muscat, Oman, in July 2012. She was treated successfully with surgical resection and prolonged antifungal therapy (voriconazole). Physicians, including clinicians, radiologists and pathologists, should have a high index of suspicion for GIB when a patient presents with an abdominal mass and fever.