Failure to wean from cardiopulmonary bypass (CPB) is a rare but critical intraoperative challenge. Common causes include residual structural defects (causing intracardiac shunting, prosthetic valve leaks), left ventricle outflow tract obstruction, ventricular dysfunction, or vasoplegic syndrome. We present the case of a 56-year-old man with severe aortic stenosis who underwent surgical aortic valve replacement. Separation from CPB failed repeatedly due to acute right ventricular dysfunction detected on transesophageal echo. The patient was found to have a congenital anomalous high origin of the right coronary artery (RCA), likely compromised during surgery. Timely recognition and surgical revascularization of the RCA with a saphenous vein graft restored right ventricular function and facilitated successful weaning. This case highlights the importance of intraoperative echocardiography, awareness of anomalous coronary anatomy, and prompt multidisciplinary decision-making in managing difficult separation from CPB.