Abstract Introduction Gastric adenomyoma is a rare benign tumour which occurs 85% in antrum and 15% in pylorus. Although adenomyomas are benign, diagnosis is difficult as they are commonly found alongside with adenocarcinomas. Case report A 20-year-old previously healthy female presented with epigastric pain, gastric outflow obstruction features and weight loss for 3 months. Initial USS was followed by a CECT which, showed intramural mass lesion with necrotic centre arising from the inferior wall of the pre pyloric area of the stomach with acute inflammatory changes of the adjacent omental fat, giving differential diagnosis of GIST or gastrinoma at pyloric region. Subsequent upper GI endoscopy revealed a protruding pyloric mass without mucosal lesions. Unfortunately, the unavailability of EUS and biopsy posed a diagnostic hurdle. Intraoperatively, a mass intricately adhered to the transverse colon and omentum was discovered, leading to a surgical intervention involving distal gastrectomy, gastrojejunostomy, and jejunojejunostomy. Unexpectedly, histological analysis unveiled adenomyoma at the prepyloric area, characterized by Brunner’s glands, dilated glands, and heterotrophic small intestinal tissue. Discussion This rare manifestation of adenomyoma in the gastric pylorus, particularly in a young adult, highlights the challenges in accurate preoperative diagnosis. The favourable postoperative outcome prompts reflection on the potential role of advanced diagnostic tools, emphasizing the significance of EUS and biopsy in steering clear of extensive surgeries. Conclusions This case report underscores the crucial role of personalized diagnostic methods, especially in cases like ours where a rare adenomyoma mimicking other tumours.