Introduction Basidiobolomycosis is a rare fungal disease, lately appearing in the gastrointestinal system of pediatric patients. Their clinical presentation resembles that of lymphoma or granulomatous inflammations. This non-specific presentation makes Gastrointestinal Basidiobolomycosis (GIB) a diagnostic challenge. Methods We are reporting the largest series of pediatric GIB, from Saudi Arabia. 12 patients were diagnosed between January 2012 and December 2019, between the ages of 16 months and 8 years. Results The most common symptoms were fever and abdominal pain. Further examination revealed an abdominal mass. Biopsy of the mass was the mainstay of diagnosis, with histological findings of typical filamentous fungal hyphae and zygospores, surrounded by eosinophils. Conclusion Role of surgery was limited to establishing the diagnosis and dealing with complications. Antifungal medication was the cornerstone of treatment in all our patients. Three of our patients were exceptional with complications such as entero-cutaneal fistula, entero-enteric fistula and short bowel syndrome. These complications have not been previously reported. We have discussed the challenges related to their management. The diagnosis of GIB in pediatric patients with abdominal mass, needs a high index of suspicion. We believe outcome depends on the severity of disease, involvement of surrounding tissues and presence of complications at the time of diagnosis.