Purpose The aim of this study was to evaluate the diagnostic performance of Inhance 3D Velocity (I3DV) in intracranial venous thrombosis and investigate the possible impact of venous sinus hypoplasia/aplasia on false thrombosis diagnosis made with I3DV. Methods This study included 540 patients. Contrast-enhanced magnetic resonance venography combined with conventional sequences was considered the gold standard test (GST), while I3DV was considered as diagnostic test. We accessed the diagnostic success of I3DV for intracranial venous thrombosis detection, thrombosed vessel identification, and total/partial thrombus distinction. The possible relationship between false-positive thrombus diagnosed by I3DV and venous sinus hypoplasia or aplasia diagnosed by GST was investigated. Results The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of I3DV in the detection of intracranial venous thrombosis were 95.7%, 92.1%, 64.1%, 99.3%, and 92.6%, respectively. A significant association was observed between I3DV and GST in terms of thrombosis detection and total/partial thrombus distinction (p < 0.001). A significant relationship was observed between false-positive thrombosis diagnosis in I3DV and hypoplasia in the left transverse sinus (p < 0.001). Conclusion Intracranial venous thrombosis may be diagnosed faster and more accurately than traditional phase contrast magnetic resonance angiography in I3DV. This technique can be used in situations where contrast medium application is contraindicated. As in other non-contrast magnetic resonance venography techniques, left transverse sinus hypoplasia can be diagnosed as a thrombosed vessel in I3DV.