Kidney organoids derived from human pluripotent stem cells exhibit glomerular- and tubular-like compartments that are largely avascular and immature in static culture. Here, we report an in vitro method for culturing kidney organoids under flow on millifluidic chips, which greatly expands their endogenous pool of endothelial progenitor cells (EPCs) and generates vascular networks with perfusable lumens surrounded by mural cells. Vascularized kidney organoids cultured under flow exhibit more mature podocyte and tubular compartments with enhanced cellular polarity and adult gene expression, compared to static controls. However, the association of vessels with these compartments is reduced upon disrupting the endogenous VEGF gradient. Glomerular vascular development progresses through intermediate stages akin to the embryonic mammalian kidney’s formation of capillary loops abutting foot processes. The ability to induce substantial vascularization and morphological maturation of kidney organoids in vitro under flow opens new avenues for studying kidney development, disease, and regeneration.