Purpose Benchmarking of flow and perfusion MR techniques on standardized phantoms can facilitate the use of advanced angiography and perfusion‐mapping techniques across multiple sites, field strength, and vendors. Here, MRA and perfusion mapping by arterial spin labeling (ASL) using Fourier transform (FT)–based velocity‐selective saturation and inversion pulse trains were evaluated on a commercial perfusion phantom. Methods The FT velocity‐selective saturation–based MRA and FT velocity‐selective inversion–based ASL perfusion imaging were compared with time‐of‐flight and pseudo‐continuous ASL at 3 T on the perfusion phantom at two controlled flow rates, 175 mL/min and 350 mL/min. Velocity‐selective MRA (VSMRA) and velocity‐selective ASL (VSASL) were each performed with three velocity‐encoding directions: foot–head, left–right, and oblique 45°. The contrast‐to‐noise ratio for MRA scans and perfusion‐weighted signal, as well as labeling efficiency for ASL methods, were quantified. Results On this phantom with feeding tubes having only vertical and transverse flow directions, VSMRA and VSASL exhibited the dependence of velocity‐encoding directions. The foot–head‐encoded VSMRA and VSASL generated similar signal contrasts as time of flight and pseudo‐continuous ASL for the two flow rates, respectively. The oblique 45°–encoded VSMRA yielded more uniform contrast‐to‐noise ratio across slices than foot–head and left–right‐encoded VSMRA scans. The oblique 45°–encoded VSASL elevated labeling efficiency from 0.22‐0.68 to 0.82‐0.90 through more uniform labeling of the entire feeding tubes. Conclusion Both FT velocity‐selective saturation–based VSMRA and FT velocity‐selective inversion–based VSASL were characterized on a commercial perfusion phantom. Careful selection of velocity‐encoding directions along the major vessels is recommended for their applications in various organs.