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Abstract The present study systemically investigated the influence of gated/non-gated sequences, velocity encoding (VENC), and spatial resolution on blood flow, wall shear stress (WSS), and artery area evaluations when scanning the common carotid artery (CCA) in rats using phase-contrast magnetic resonance imaging (PC-MRI). We first tested whether or not non-gated PC-MRI was appropriate for evaluating blood flow and WSS in rats. For both gated and non-gated techniques, VENC values in the range of 60–120 cm/s with an interval of 10 cm/s were also tested. Second, we optimized the in-plane resolution of PC-MRI for blood flow and WSS measurements. Results showed the usage of a gated instrument can provide more reproducible assessments, whereas VENC had an insignificant influence on all hemodynamic measurements (all P > 0.05). Lower resolutions, such as 0.63 mm, led to significant overestimations in blood flow and artery area quantifications and to an underestimation in WSS measurements (all P < 0.05). However, a higher resolution of 0.16 mm slightly increased measurement variation. As a tradeoff between accuracy and scan time, we propose a gated PC-MRI sequence with a VENC of 120 cm/s and a resolution of 0.21 mm to be used to extract hemodynamic information about rat CCA.