The top of your stomach may hurt because of heartburn or reflux of stomach acid into the bottom portion of the esophagus. The stomach is divided into different regions. The top of the stomach is called the "cardia" and this region connects to the esophagus, the tube that food travels through. The cardia can cause pain when stomach acid splashes up through the opening between the esophagus and stomach and burns the lower end of the esophagus.