Co-existing pyloric submucosal masses with hypertrophic pyloric stenosis (HPS) are very rare and treating these lesions is always a problem. A 20-day-old boy presented with recurrent episodes of projectile non-bilious vomiting lasting for 5 days. HPS was suspected due to the presenting age and the symptoms. The sonography demonstrated not only circumferential wall thickening of the pylorus, but also a pyloric submucosal mass. At laparotomy, a 0.8 cm sized pyloric submucosal mass was identified along with a hypertrophied pylorus. Pyloric excision was performed due to the possibility of sustaining the symptoms and malignancy. The pathological report of the submucosal mass was ectopic pancreas. Coexisting pyloric lesions can be diagnosed along with HPS, and surgical excision, not just pyloromyotomy, should be considered in these circumstances. To the best of our knowledge, this is the first case report of pyloric ectopic pancreas and HPS to be diagnosed concurrently.