A live-stranded harbor porpoise Phocoena phocoena was found on the west coast of the Dutch island Texel (North Sea) and transported to a rehabilitation center for small cetaceans, where it underwent a veterinary health check. Cardiac auscultation revealed a systolic cardiac murmur with the point of maximal intensity in the right hemithorax with an intensity of IV out of VI. Transthoracic echocardiography revealed a congenital ventricular septal defect with left-to-right shunting. Because the left atrium was not dilated according to the reference range of canine left atrium to aortic ratio, the presence of congestive heart failure was considered very unlikely. Therefore, this congenital cardiac anomaly was thought to be a clinically non-relevant incidental finding and would not explain the weakness, coughing, anorexia, vomiting, and diarrhea. Because the animal was still unable to swim or eat by itself after 2 wk of supportive care, it was euthanized. Post-mortem examination confirmed the presence of a ventricular septal defect. The weight of the heart relative to the animal’s length was greater than expected, using linear regression analysis on the lengths and cardiac weights of 71 other stranded wild harbor porpoises without macroscopic cardiac pathologic changes. This finding suggests that the left ventricle had an eccentric hypertrophy because of volume overload resulting from the intracardiac shunt. This is the first report of a congenital cardiac anomaly and its ante-mortem diagnosis in this species. Data presented for the other 71 harbor porpoises may provide reference values for this species.