Background Direct evidence of intimal flaps, double lumen and intramural haematomas (IMH) is difficult to detect on conventional angiography in most intracranial vertebrobasilar dissecting aneurysms (VBDAs). Our purpose was to assess the value of three-dimensional high-resolution magnetic resonance vessel wall imaging (3D HRMR VWI) for identifying VBDAs. Methods Between August 2013 and January 2016, consecutive patients with suspicious VBDAs were prospectively enrolled to undergo catheter angiography and VWI (pre- and post-contrast). The lesion was diagnosed as definite VBDA when presenting direct signs of dissection; as possible when only presenting indirect signs; and as segmental ectasia when there was local dilation and wall thickness similar to adjacent normal artery's without mural thrombosis. Results Twenty-one patients with 27 lesions suspicious for VBDAs were finally included. Based on findings of VWI and catheter angiography, definite VBDA was diagnosed in 25 and 7 lesions (92.6%, vs 25.9%, p < 0.001), respectively; possible VBDA in 0 and 20 (0 vs 74.1%), respectively; and segmental ectasia in 2 and 0 (7.4% vs 0%), respectively. On VWI and catheter angiography, intimal flap was detected in 21 and 7 lesions (77.8% vs 25.9%, p = 0.001), respectively; double lumen sign in 18 and 7 (66.7% vs 25.9%, p = 0.003), respectively; and IMH sign in 14 and 0 (51.9% vs 0), respectively. Conclusions 3D HRMR VWI could detect direct dissection signs more frequently than catheter angiography. This may help obtain definite diagnosis of intracranial VBDAs, and allow accurate differentiation between dissecting aneurysm and segmental ectasia as well. Further prospective study with larger sample was required to investigate the superiority of HRMR VWI for definite diagnosis of intracranial VBDAs than catheter angiography.