Background: Duodenal duplication cysts, though rare, require prompt recognition and precise treatment due to their distinctive clinical challenges. Diagnosis depends on factors like size, location, and proximity to surrounding structures, necessitating a tailored approach for optimal outcomes. Case Report: We present a 13-year-old girl with a duodenal duplication cyst, manifesting as persistent abdominal pain and nausea. Radiological investigations, including contrast-enhanced computed tomography and ultrasound, guided the diagnosis. The cyst's non-communicating nature and its close association with the gut lumen prompted a submucosal resection during surgery, preserving duodenal continuity. Conclusion: This case emphasizes the complexity of duodenal duplication cyst management. Surgical decisions are intricately tied to the individual characteristics of the cyst, emphasizing total resection as the ideal management. As we navigate this rare entity, insights gained contribute to refining diagnostic and therapeutic paradigms for optimal patient care.