Acute kidney injury (AKI), a condition marked by rapid loss of kidney function, carries significant morbidity and often progresses to chronic kidney disease (CKD). Ischemia-reperfusion injury (IRI) is a major pathogenic driver of AKI. To elucidate the molecular mechanisms underlying IRI-induced AKI and its progression to CKD, we performed comprehensive proteomic and phosphoproteomic profiling of kidney tissues. Using high-resolution mass spectrometry, we confidently quantified over 7,500 proteins and 4,400 non-redundant phosphoproteins, providing a systems-level view of the extensively remodeled kidney proteome and phosphoproteome post-IRI. Our dataset reveals dynamic alterations in key signaling pathways associated with AKI-to-CKD transition, offering unprecedented molecular insights into disease progression. This resource will facilitate the discovery of therapeutic targets to mitigate IRI-induced kidney damage and its chronic sequelae.