Recent reports indicate that the complement C5a/C5aR pathway and progranulin (PGRN) deficiency both contribute to ischemia-reperfusion (IR)-induced acute kidney injury. However, the underlying relationship between the C5a/C5aR signaling pathway and PGRN expression during acute kidney injury is poorly understood. In this study, we showed that C5aR expression was significantly upregulated after renal IR, and that C5aR deficiency led to a marked increase in PGRN expression and a significant reduction in tubular damage and production of inflammatory cytokines. In accordance with these results, recombinant C5a caused downregulation of PGRN protein and mRNA levels in renal tubular epithelial cells (HK-2 cells), which could be negated by disruption of C5a/C5aR signaling by the C5aR antagonist, as confirmed by immunofluorescence, western blotting, and quantitative real-time PCR. Moreover, C5aR deficiency resulted in attenuated NF-κB expression 24 h after IR, and recombinant C5a potentiated TNFα-induced NF-κB activation in HK-2 cells. Inhibition of NF-κB activation reversed C5a-induced downregulation of PGRN expression. Our results show for the first time that the complement C5a/C5aR pathway aggravates IR-induced acute kidney injury by suppressing PGRN expression and confirm that suppression of PGRN expression is associated with increased NF-κB activation induced by C5a.