Pump thrombosis is a rare and infrequent complication of HeartMate III left ventricular assist device (LVAD). While there are reports of pump thrombosis in the postoperative period, to our knowledge, there have been no prior reports on pump thrombosis in the intraoperative period. Here we present a case of a 24-year-old female who required HeartMate III LVAD implantation for progressive heart failure and the intraoperative period was complicated with pump thrombosis (PT). Managing PT in the intraoperative period is challenging and time-sensitive because of its rare occurrence and paucity of recommendations in diagnosing the PT.