Recent studies have implicated RNF213 mutations in the pathogenesis of moyamoya disease (MMD). However, the underlying mechanism of disease development is not fully elucidated. Nonetheless, a possible relationship between vascular morphology and hemodynamics related with MMD has been proposed. Here, we aimed to investigate the relationship between a variant of RNF213 and the morphology of the internal carotid artery (ICA). We enrolled bilateral MMD patients who had undergone genetic testing for RNF213. Patients were divided into mutant and wild-type groups. Six anatomy-specific three-dimensional coordinates were collected using magnetic-resonance angiography. From these, five vectors between two adjacent points and four angles between two adjacent vectors were calculated. The tortuosity was defined as the ratio between the actual and the linear length of the ICAs. Among 58 patients, 44 and 14 belonged to the mutant and wild-type groups, respectively. The tortuosity of ICAs was significantly lower in the mutant group (p = 0.010). The change in blood flow direction was more prominent in the wild-type group (p = 0.002). The tortuosity was significantly lower in MMD patients than normal controls (p < 0.001). Our results indicate that RNF213 could play a role in the lower tortuosity observed in patients with RNF213 mutation.