Single-isocenter (SI) noncoplanar volumetric modulated arc therapy (NC-VMAT) has been widely used in stereotactic radiosurgery (SRS) or hypofractionated stereotactic radiotherapy (HSRT) for multiple brain metastases (BMs). However, it is critical to verify patient positioning at a noncoplanar couch angle. This study aimed to compare the noncoplanar setup discrepancies between kilo-voltage/mega-voltage image (kV/MV) orthogonal image pairs with a 2-dimensional/3-dimensional (2D/3D) matching mode and noncoplanar cone-beam computed tomography (NC-CBCT) with a 3D/3D matching mode in SI NC-VMAT HSRT for multiple BMs. Twenty patients with multiple BMs [2-5] who underwent SI NC-VMAT HSRT were enrolled in this study. Prior to each noncoplanar field delivery, both kV/MV orthogonal image pairs and NC-CBCT were used to determine setup errors. The setup error values reported by NC-CBCT were defined as the gold standard and compared to those reported by kV/MV orthogonal image pairs. The Bland-Altman analysis method was utilized to assess the agreement of the two positioning modalities. In total, 104 kV/MV image pairs and NC-CBCT scans were acquired. The mean setup error differences (SEDs; absolute values) between the two positioning systems were 0.17 mm, 0.21 mm, 0.16 mm, 0.22°, 0.18°, and 0.17° in the vertical, longitudinal, lateral, yaw, pitch, and roll directions, respectively. The maximum SEDs regarding translation and rotation occurred in the longitudinal and yaw directions at 0.60 mm and 0.8°, respectively. Bland-Altman analysis showed excellent agreement between the two positioning modalities, and the 95% limits of agreement (LOAs) never exceeded 0.6 mm and 0.6° in the translational and rotational directions, respectively. Only 4.80% of SEDs exceeded the tolerance of 0.5 mm/0.5°. Orthogonal kV/MV image pairs with 2D/3D matching mode could provide comparable accuracy for noncoplanar positioning as NC-CBCT with 3D/3D matching mode.