A variety of protocols have been developed that demonstrate the capability to differentiate human pluripotent stem cells (hPSCs) into kidney structures. Our goal was to develop a high-efficiency protocol to generate nephron progenitor cells (NPCs) and kidney organoids to facilitate applications for tissue engineering, disease modeling and chemical screening. Here, we describe a detailed protocol resulting in high-efficiency production (80–90%) of NPCs from hPSCs within 9 d of differentiation. Kidney organoids were generated from NPCs within 12 d with high reproducibility using 96-well plates suitable for chemical screening. The protocol requires skills for culturing hPSCs and careful attention to morphological changes indicative of differentiation. This kidney organoid system provides a platform for studies of human kidney development, modeling of kidney diseases, nephrotoxicity and kidney regeneration. The system provides a model for in vitro study of kidney intracellular and intercompartmental interactions using differentiated human cells in an appropriate nephron and stromal context.