Abstract Background The relationship between intracranial vessel configuration and wall features remains poorly investigated. Therefore, we aimed to investigate the relationship between the distal and proximal anatomical configuration of basilar artery (BA) and BA vessel wall features on high-resolution magnetic resonance imaging (HRMRI). Methods From September 2014 to January 2017, patients with suspected symptomatic intracranial arterial stenosis underwent HRMRI. Patients with severe BA stenosis were selected for this prospective study and divided into two groups corresponding to complete and incomplete BA configuration based on characteristics of the bilateral vertebral arteries and posterior cerebral arteries. Culprit blood vessel wall features on HRMRI included plaque enhancement, intraplaque hemorrhage, remodeling patterns, and plaque distribution. Culprit vessel wall features were compared between patients in the complete and incomplete BA configuration groups. Results Among the 298 consecutively enrolled patients, 34 had severe BA stenosis. Twenty patients had complete anatomical BA configuration and another 14 of them displayed incomplete configuration. There were no significant differences in vessel wall features between the complete and incomplete configuration patient groups. However, the proximal configuration of BA was associated with intraplaque hemorrhage (p = 0.002) while the distal configuration of BA correlated with strong enhancement of BA plaque (p = 0.041). Conclusions No association was found between the complete and incomplete BA configuration groups and blood vessel wall features. The proximal configuration of BA was related with intraplaque hemorrhage and the distal configuration of BA was associated with strong plaque enhancement. Further studies are warranted to confirm these findings. Trial registration URL: Unique identifier: NCT02705599 (March 10, 2016).