This study aimed to analyze the hemodynamic features of the offending artery at sites of neurovascular compression (NVC) using computational fluid dynamics (CFD). A total of 23 patients who underwent microvascular decompression (MVD) for primary trigeminal neuralgia (TN) between January 2015 and December 2016 were enrolled in this study. The compressing vessel at the NVC site was identified microsurgically in all cases, and patients were divided into two groups based on the intraoperative findings: (1) the arterial NVC group and (2) the non-arterial NVC control group. A 3D surface model of the structures surrounding the NVC was created using preoperative magnetic resonance imaging (MRI), and CFD analysis was performed for the target artery. In addition to standard parameters, such as the wall shear stress (WSS), flow velocity, and pressure, we calculated the WSS ratio (WSSR) by dividing the WSS at the NVC by the mean WSS of the target. Arterial compression was observed intraoperatively in 13 patients. The mean WSSR of the arterial NVC group was significantly higher than that of the control group (2.36 ± 1.00 vs. 1.18 ± 0.73, P <0.05). There were no significant intergroup differences in the other calculated parameters. High WSSR, which indicates elevated WSS at the sites of NVC, was identified as a unique parameter of arterial compression that may contribute to TN. CFD could be a useful clinical tool in determining the target of MVD under preoperative conditions.