We present a unique presentation of Crohn's disease in a 25-year-old male with a 3-month history of progressive gastric outlet obstruction symptoms including reflux, vomiting, postprandial pain and weight loss, with no other symptoms. Multiple imaging investigations as well as gastroscopic biopsies revealed a non-specific prepyloric lesion, without evidence of malignancy. A distal gastrectomy was performed. Subsequent histological evaluation revealed gastroduodenal Crohn's disease. Follow-up revealed no evidence of disease elsewhere in the gastrointestinal system or systemically. While it is not uncommon for Crohn's disease to involve the stomach and duodenum, it is rare for gastroduodenal disease to be the initial presentation. Isolated gastroduodenal Crohn's disease typically presents with non-specific gastritis-like symptoms over a number of years. This patient had a unique course of Crohn's disease with rapid onset of symptoms, predominantly relating to gastric outlet obstruction and no prior or subsequent history of gastrointestinal symptoms.