Knowledge of CBF in neonates may provide valuable information in many pathological conditions. When applied to very young children, CBF mapping using arterial-spin-labeling (ASL) MRI suffers from low signal-to-noise ratio and poor quantification, whereas phase-contrast (PC) MRI may provide reliable estimation of global CBF. This study aimed to optimize the PC-MRI protocol for future applications in neonates. By comparing the cardiac-gated and non-gated implementations, we found non-gated PC-MRI could provide accurate CBF measurement with shorter scan time. We also found lower imaging resolution would over-estimate CBF, and therefore recommend the use of 0.3mm resolution with 6 averages in neonates.