Four-dimensional (4D) flow magnetic resonance imaging (MRI) allows three-dimensional velocity encoding to measure blood flow in a single scan, regardless of the intracranial artery direction. We compared blood flow velocity quantification by non-contrast 4D flow MRI and by transcranial Doppler ultrasound (TCD), the most widely used modality for measuring velocity. Twenty-two patients underwent both TCD and non-contrast 4D flow MRI. The mean time interval between TCD and non-contrast 4D flow MRI was 0.7 days. Subsegmental velocities were measured bilaterally in the middle cerebral and basilar arteries using TCD and non-contrast 4D flow MRI. Intracranial velocity measurements using TCD and non-contrast 4D flow MRI demonstrated a strong correlation in the bilateral M1, especially at the proximal segment (right r = 0.74, left r = 0.78; all p < 0.001). Mean velocities acquired with 4D flow MRI were approximately 8 to 10% lower than those acquired with TCD according to the location of M1. Intracranial arterial flow measurements estimated using non-contrast 4D flow MRI and TCD showed strong correlation. 4D flow MRI enables simultaneous assessment of vascular morphology and quantitative hemodynamic measurement, providing three-dimensional blood flow visualization. 4D flow MRI is a clinically useful sequence with a promising role in cerebrovascular disease.