Background Acute kidney injury following ischemia−reperfusion remains a substantial perioperative challenge lacking effective treatment. p21-activated kinase 4 (PAK4), a downstream effector of Rho GTPase, has been explored in hepatic ischemia−reperfusion injury, but its role in renal ischemia−reperfusion is unknown. Methods Wild-type and proximal tubule-specific Pak4 knockout mice underwent 25 min of ischemia followed by 24 h of reperfusion injury. Primary tubular cells and HK-2 cells were exposed to hypoxia−reoxygenation injury to investigate the in vitro impact of PAK4. Selective degradation of PAK4 was employed using proteolysis-targeting chimeras (PROTAC) to ameliorate acute kidney injury. Results Post-ischemia−reperfusion, the expression of PAK4 was upregulated through hypoxia-inducible factor 1 alpha in mouse kidneys. Deletion of PAK4 in proximal tubule cells, but not in myeloid cells, significantly mitigated ischemia−reperfusion-induced acute kidney injury, as evidenced by decreased levels of blood urea nitrogen, creatinine, tubular necrosis, apoptosis, macrophage infiltration, and lipid accumulation compared to control mice. Further investigation revealed that PAK4 phosphorylated glutathione peroxidase 3 at T47, leading to its proteasomal degradation. Additionally, pretreatment of mice with the PAK4 PROTAC preserved glutathione peroxidase 3 and enhanced fatty acid β-oxidation, thereby protecting against acute kidney injury. In kidney tissues from people with a kidney transplant, elevated levels of PAK4 protein and phosphorylation of glutathione peroxidase 3 at T47 were observed. Conclusions Renal tubular PAK4 contributes to tissue damage during ischemia−reperfusion injury, while PAK4 PROTAC mitigates ischemia−reperfusion injury by reducing oxidative stress and promoting fatty acid β-oxidation.