Introduction: Trendelenburg position (TP) is used to transport gaseous emboli away from the cerebral region during cardiac surgery. However, TP effectiveness has not been fully considered when combined with varying the cardiopulmonary bypass (CPB) flow. This study simulated the supine and TP at different pump flows and assessed the trapped emboli and embolic load entering the aortic arch branch arteries (AABA). Methods: A computational fluid dynamics (CFD) approach used a centrally cannulated adult patient-specific aorta model replicating a CPB circuit. Air emboli of 0.1 mm, 0.5 mm, and 1.0 mm (n = 700 each) were injected into the aorta placed in the supine position (0°) and the TP (−20°) at 2 L/min and 5 L/min. The number of emboli entering the AABA were compared. An aortic phantom flow experiment was performed to validate air bubble behaviour. Results: TP at 5 L/min had the lowest 0.1 mm mean (±SD) embolic load compared to the supine 2 L/min (55.3 ± 30.8 vs 64.3 ± 35.4). For both the supine and TP, the lower flow of 2 L/min had the highest number of simulated trapped emboli in higher elevated regions than at 5 L/min (541 ± 185 and 548 ± 191 vs 520 ± 159 and 512 ± 174), respectively. The flow experiment demonstrated that 2 L/min promoted bubble coalescence and high amounts of trapped emboli and 5 L/min transported air emboli away from the AABA. Conclusions: TP effectiveness was improved by using CPB flow to manage air emboli. These results provide insights for predicting emboli behaviour and improving emboli de-airing procedures.