A vertebral artery (VA) terminating in a posterior inferior cerebellar artery (PICA) is often considered to be a normal variation associated with VA hypoplasia. We aimed to investigate the clinical significance of this cerebrovascular variant. A total of 80 patients with clinically evident cerebrovascular events in posterior circulation were examined by duplex sonography and magnetic resonance angiography (MRA). Eighty healthy subjects who had MRA check-up were recruited as controls. PICA termination of the VA (PICA-VA) was identified as the VA not communicating with the basilar artery (BA) but ending into a PICA. We compared the prevalence of PICA-VA and associated hemodynamic parameters between the patients with and without PICA-VA, and investigated their relationships with VA hypoplasia. The prevalence of PICA-VA was higher in the patient group than in the controls (18.7% vs. 6.3%, p = 0.015). Most measurements (73.3%) of PICA-VA did not fit the criteria of VA hypoplasia. In comparison with the non-PICA-terminating group, the PICA-VA has a smaller diameter (3.7 ± 0.7 mm vs. 3.0 ± 0.5 mm, p < 0.001), lower mean velocity (241 ± 100 mm/sec vs. 164 ± 88 mm/sec, p < 0.01), and higher pulsatility index (1.3 ± 0.5 vs. 1.9 ± 0.6, p < 0.001). Moreover, a smaller diameter of the BA (3.2 ± 0.5 mm vs. 2.5 ± 0.9 mm, p = 0.004) and the posterior cerebral artery (PCA) (2.0 ± 0.1 mm vs. 1.6 ± 0.1 mm, p = 0.006) were also noted in the PICA-VA group. The higher prevalence of PICA-VA in the patient group with smaller diameter of VA, BA and PCA reflected its clinical significance, suggesting that PICA-VA may have a detrimental impact on cerebral hemodynamics. However, the sample is small, and further studies are needed with larger sample size for confirmation.