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To develop a Fourier-transform based velocity-selective inversion (FT-VSI) pulse train for velocity-selective arterial spin labeling (VSASL).This new pulse contains paired and phase cycled refocusing pulses. Its sensitivities to B0/B1 inhomogeneity and gradient imperfections such as eddy currents were evaluated through simulation and phantom studies. Cerebral blood flow (CBF) quantification using FT-VSI prepared VSASL was compared with conventional VSASL and pseudocontinuous ASL (PCASL) at 3 Tesla.Simulation and phantom results of the proposed FT-VSI pulse train demonstrated excellent robustness to B0/B1 field inhomogeneity and eddy currents. The estimated CBF of gray matter and white matter for the FT-VSI prepared VSASL, averaged among eight healthy volunteers, were 49.5 ± 7.5 mL/100 g/min and 14.8 ± 2.4 mL/100 g/min, respectively. Excellent correlation and agreement between the FT-VSI method and conventional VSASL and PCASL were found. The averaged signal-to-noise ratio (SNR) value in gray matter of the FT-VSI method was 39% higher than VSASL using conventional double refocused hyperbolic tangent pulses and 9% lower than PCASL.A novel FT-VSI pulse train was demonstrated to be a suitable labeling module for VSASL with robustness of velocity-selective profile to B0/B1 field inhomogeneity and gradient imperfections. Compared with conventional VSASL, FT-VSI prepared VSASL produced consistent CBF maps with higher SNR values. Magn Reson Med 76:1136–1148, 2016. © 2015 Wiley Periodicals, Inc.