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Genetic regulation of vascular patterning is not fully understood. Here, we report a novel gene, <i>gtpbp1l</i> (<i>GTP-binding protein 1-like</i>), that regulates vascular development in zebrafish. Amino acid sequence comparison and a phylogenetic study showed that <i>gtpbp1l</i> is conserved in vertebrates. <i>Gtpbp1l</i> mRNA is expressed in the vasculature during embryogenesis. Knockdown of <i>gtpbp1l</i> by morpholino impairs the patterning of the intersegmental vessel (ISV) and caudal vein plexus (CVP), indicating the role of <i>gtpbp1l</i> in vasculature. Further apoptosis assays and transgenic fish tests suggested that vascular defects in <i>gtpbp1l</i> morphants are not due to cell death but are likely caused by the impairment of migration and proliferation. Moreover, the altered expression of vessel markers is consistent with the vascular defects in <i>gtpbp1l</i> morphants. Finally, we revealed that <i>gtpbp1l</i> is regulated by VEGF/notch and BMP signaling. Collectively, these findings showed that <i>gtpbp1l</i> plays a critical role in vascular patterning during zebrafish development.