The objective of this Case Report was to describe the clinical manifestation and postmortem findings of a horse evaluated for recurrent colic diagnosed with pyloric aplasia and an ectopic duodenal papilla. 13-year-old Quarter Horse gelding. The horse was presented to a referral center for signs of colic that were unresponsive to management on the farm. No abnormalities were noted on rectal palpation; however, upon passage of a nasogastric tube, 31 L of net gastric reflux was obtained. Gastroscopy noted grade IV squamous ulceration and moderate glandular ulceration, severe gastric dilatation, an abnormally positioned gastric outflow tract, and an ectopic duodenal papilla leaking bile-like fluid directly into the stomach. The horse was initially treated with gastroprotectants, promotility agents, and dietary modifications. Following treatment failure and repeated episodes of colic with increasing severity, the horse was euthanized and a necropsy performed. At necropsy, it was confirmed that the aboral aspect of the stomach formed a dilated pouch and continued directly into the proximal duodenum with no discernible pyloric sphincter. The area of the pylorus was delineated by a faint indentation. The ectopic duodenal papilla was traced to the liver. Congenital gastric abnormalities, even in adult horses, should be considered as differential diagnoses when investigating horses presenting with a history of chronic colic. Neither pyloric aplasia nor an ectopic duodenal papilla have been described in the equine literature, and this Case Report raises awareness of the presence of such malformations and their manifestations.