Kidneys are highly vascularized and contain many distinct vascular beds. However, the origins and roles of developing renal endothelial cells in the formation of the kidney are unclear. We have shown that the Foxd1-positive renal stroma gives rise to endothelial marker expressing progenitors that are incorporated within a subset of peritubular capillaries; however, the significance of these cells is unclear. The purpose of this study was to determine whether deletion of Flk1 in the Foxd1 stroma was important for renal development. To that end, we conditionally deleted Flk1 (critical for endothelial cell development) in the renal stroma by breeding floxed Flk1 mice (Flk1^fl/fl) with Foxd1cre mice to generate Foxd1cre; Flk1^fl/fl (Flk1^ST-/-) mice. We then performed FACsorting, histological, morphometric and metabolic analyses of Flk1^ST-/- versus control mice. We confirmed decreased expression of endothelial markers in the renal stroma of Flk1^ST-/- kidneys via Flow sorting and immunostaining, and upon interrogation of embryonic and postnatal Flk1^ST-/- mice we found they had dilated peritubular capillaries. Three-dimensional (3D) reconstructions showed reduced ureteric branching, and fewer nephrons in developing Flk1^ST-/- kidneys versus controls. Juvenile Flk1^ST-/- kidneys displayed renal papillary hypoplasia and a paucity of collecting ducts. 24-hour urine collections revealed that postnatal Flk1^ST-/- mice had urinary concentrating defects. Thus, while lineage-tracing revealed that the renal cortical stroma gave rise to a small subset of endothelial progenitors, these Flk1 expressing stromal cells are critical for patterning the peritubular capillaries. Also, loss of Flk1 in the renal stroma leads to non-autonomous patterning defects in ureteric lineages.