The murine cell surface protein Crry (complement receptor 1-related protein/gene y) is a key complement regulator with similar activities to human membrane cofactor protein (MCP) and decay-accelerating factor. MCP has a critical role in preventing complement-mediated tissue injury and its mutation has been implicated in several human kidney diseases. The study of Crry in mice has relevance to understanding MCP activity in human diseases; however, such efforts have been hampered by the embryonic lethality phenotype of Crry gene knockout. Here we used a conditional gene-targeting approach and deleted Crry from the mouse proximal tubular epithelial cells where Crry is prominently expressed. Absence of Crry from proximal tubular epithelial cells resulted in spontaneous C3 deposition on the basolateral surface but no apparent renal disease in unchallenged mice. However, mice deficient in Crry on proximal tubular epithelial cells developed exacerbated renal injury when subjected to renal ischemia-reperfusion, showing increased blood urea nitrogen levels, higher tubular injury scores, more tubular epithelial cell apoptosis, and inflammatory infiltrates. Renal ischemia-reperfusion injury in the Crry conditional knockout mice was prevented by blocking C3 and C5 activation using an anti-properdin or anti-C5 monoclonal antibody (mAb), respectively. Thus, Crry has a critical role in protecting proximal tubular epithelial cells during ischemia-reperfusion challenge. Our results highlight the latent risk for inflammatory kidney injury associated with defects in membrane complement regulators.