The masticatory function of patients with skeletal anterior open bite (OPEN) is reported to be impaired compared with that of patients with normal occlusion (NORM). In this study, we compared brain blood flow (BBF) in patients with OPEN and NORM and investigated the factors related to BBF during mastication in patients with OPEN. The study included 17 individuals with NORM and 33 patients with OPEN. The following data were collected: number of occlusal contacts, jaw movement variables during mastication, and BBF measured with functional near-infrared spectroscopy during chewing. The number of occlusal contacts, maximum closing and opening speeds, closing angle, and vertical amplitude were smaller in the OPEN than in the NORM group. Interestingly, BBF increased less in the OPEN group. Correlation analysis revealed that several parameters, including number of occlusal contacts and closing angle, were correlated with changes in BBF during mastication. These results suggest that not only occlusion but also jaw movement variables and factors related to masticatory muscles contribute to the chewing-related increase in BBF. In conclusion, BBF increases less during mastication in patients with OPEN than in those with NORM. In addition, the higher increase in BBF is correlated with jaw movement. Together, we discovered that OPEN exhibits significant adverse effects not only on masticatory function but also on brain function.