Promoting adaptive repair in acute kidney injury (AKI) is an effective strategy to prevent the progression from AKI to chronic kidney disease. However, the mechanisms involved in renal repair after AKI remain unclear. In this study, we investigated the role of hypoxia-inducible factor (HIF), an important regulator of ischemic and hypoxic injury, in AKI during the repair phase. We established mouse models of ischemia-reperfusion injury-induced AKI with adaptive repair or maladaptive repair. We found that after injury, activation of HIF in the adaptive repair group was rapid, whereas in the maladaptive repair group HIF activation was relatively delayed, and its expression was significantly lower than that in the adaptive repair group during the early repair phase. To further investigate the mechanism of HIF, we regulated the expression of HIF-1α and HIF-2α in HK-2 cells and EA.hy926 cells, respectively. Silencing HIF expression reduced proliferation and increased apoptosis in cells injured by hypoxia/reoxygenation. Self-healing ability was further reduced due to the downregulation of HIF. Moreover, HIF overexpression had the opposite effect. HIF increased the expression of β-catenin and its downstream target genes. Activation of Wnt/β-catenin by the small-molecule activator SKL2001 mitigated the damaging effect of HIF knockdown, whereas blockade of β-catenin with the inhibitor IWR-1-endo reduced the protective effects of HIF. In conclusion, HIF, which is highly expressed in the early stage after AKI, promotes renal repair by interacting with the Wnt/β-catenin signaling pathway.NEW & NOTEWORTHY We investigated the role of hypoxia-inducible factor (HIF) in acute kidney injury in vivo and in vitro. Expression of HIF in the adaptive repair group was more rapid and sufficient than that in the maladaptive repair group during the early repair phase. HK-2 and EA.hy926 cells treated with hypoxia/reoxygenation were used to elucidate the cross talk between HIF and the Wnt/β-catenin signaling pathway by which HIF played a renoprotective role in acute kidney injury.