Phase contrast magnetic resonance imaging (PC-MRI) and color-coded duplex ultrasonography (CDUS) are commonly used for measuring cerebral blood flow in the internal carotid (ICA) and vertebral arteries. However, agreement between the two methods has been controversial. Recent development of high spatial and temporal resolution blood vessel wall edge-detection and wall-tracking methods with CDUS increased the accuracy and reliability of blood vessel diameter, hence cerebral blood flow measurement. The aim of this study was to compare the improved CDUS method with 3 T PC-MRI for cerebral blood flow measurements. We found that cerebral blood flow velocity measured in the ICA was lower using PC-MRI than CDUS (left ICA: PC-MRI, 18.0 AE 4.2 vs. CDUS, 25.6 AE 8.6 cm/s; right ICA: PC-MRI, 18.5 AE 4.8 vs. CDUS, 26.6 AE 6.7 cm/s, both p < 0.01). However, ICA diameters measured using PC-MRI were larger (left ICA: PC-MRI, 4.7 AE 0.50 vs. CDUS, 4.1 AE 0.46 mm; right ICA: PC-MRI, 4.5 AE 0.49 vs. CDUS, 4.0 AE 0.45 mm, both p < 0.01). Cerebral blood flow velocity measured in the left vertebral artery with PC-MRI was also lower than CDUS, but no differences in vertebral artery diameter were observed between the methods. Dynamic changes and/ or intrinsic physiological fluctuations may have caused these differences in vessel diameter and velocity measurements between the methods. However, estimation of volumetric cerebral blood flow was similar and correlated between the methods despite the presence of large individual differences. These findings support the use of CDUS for cerebral blood flow measurements in the ICA and vertebral artery.