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Surgical planning has shown great potential for optimizing outcomes for patients affected by single ventricle (SV) malformations. Phase-contrast magnetic resonance imaging (PC-MRI) is the routine technique used for flow acquisition in the surgical planning paradigm. However, PC-MRI may suffer from possible artifacts in certain cases; furthermore, this technology may not be readily available for patients in low and lower-middle-income countries. Therefore, this study aims to investigate the effectiveness of using Doppler echocardiography (echo-Doppler) for flow acquisitions of SV surgical planning. This study included eight patients whose blood flow data was acquired by both PC-MRI and echo-Doppler. A virtual surgery platform was used to generate two surgical options for each patient: (1) a traditional Fontan conduit and (2) a Y-graft. Computational fluid dynamics (CFD) simulations were conducted using the two flow acquisitions to assess clinically relevant hemodynamic metrics: indexed power loss (iPL) and hepatic flow distribution (HFD). Differences exist in flow data acquired by PC-MRI and echo-Doppler, but no statistical significance was obtained. Flow fields, therefore, exhibit discrepancies between simulations using flow acquisitions by PC-MRI and echo-Doppler. In virtual surgery, the two surgical options were ranked based on these metrics. No difference was observed in the ranking of surgical options between using different flow acquisitions. Doppler echocardiography is an adequate alternative approach to acquire flow data for SV surgical planning. This finding encourages broader usage of SV surgical planning with echo-Doppler when MRI may present artifacts or is not available, especially in low and lower-middle-income countries.