We present a case of a 43-year-old man with Crohn’s disease who presented with epigastric and right upper quadrant abdominal pain, initially suspected to be acute cholecystitis or a Crohn’s flare-up. CT revealed a curvilinear, hyperdense foreign body adjacent to the duodenum, concerning micro-perforation. Endoscopic examination confirmed findings of a 3 cm fish bone lodged in the pylorus. Endoscopic extraction was successful without significant mucosal damage, and the patient recovered well postoperatively. This case highlights the rarity of pyloric perforation secondary to fish bone ingestion and highlights the importance of considering this diagnosis in patients presenting with unexplained acute abdominal pain, as prompt recognition and intervention are essential for favorable outcomes.