Moyamoya disease (MMD) causes intracranial arterial stenosis progression. The progression of intracranial arterial stenosis will increase the risk of ischemic cerebrovascular events. This study aims to investigate the relationship between intracranial arterial stenosis progression, vessel wall enhancement (VWE), and the recent neurological symptoms. A total of 39 MMD patients (12 male; 37.6 ± 18.0 years old) were registered in this study analysis between April 2016 and July 2018. All patients received MRI at registration and 6, 12, and 24 months post-registration. The incidence of ischemic cerebrovascular events (transit ischemic attacks or cerebral infarction) was checked until December 2018. We evaluated the relationship between the intensity of VWE, intracranial arterial stenosis, and the recent neurological symptoms. During the mean follow-up period of 13.8 ± 5.5 months, the changes in VWE were observed in 33 hemispheres (42.3%), stenosis progression was observed in 21 hemispheres (26.9%), and recent neurological symptoms occurred in 10 hemispheres (12.8%). Stenosis progression was observed in 11 hemispheres (33.3%) in the VWE(+) group and ten hemispheres (22.2%) in the VWE(−) group (p = 0.310). The recent neurological symptoms were observed in eight hemispheres (21.2%) in the VWE(+) group and two hemispheres (4.44%) in the VWE(−) group (odds ratio 6.88, 95% confidence interval 1.35–34.98, p = 0.015). The intensity of VWE sometimes changes. The changes in VWE were significantly associated with the recent neurological symptoms but not with stenosis progression.