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Bannayan-Zonana syndrome (BRRS) is a rare genetic disorder characterized by macrocephaly, numerous soft tissue and visceral hamartomas, and lipomas. Because of the risk of fatal bleeding and visceral neoplasia in adulthood, recognizing this disease is critical. We reported a new pediatric case of BRRS in an 18-month-old female infant with lipomas, macrocephaly, and gastrointestinal hamartomatous polyps that prompted ileo-ileal intussusception and protein-losing enteropathy. Patients with BRRS require a comprehensive approach. Our case is unique in its sporadic occurrence and the presence of protein-losing enteropathy as a gastrointestinal polyposis manifestation. Pediatric patients with multiple lipomas, protein-losing enteropathy, and intestinal intussusception should be assessed for BRRS.