Acute Kidney injury (AKI) is characterized by a sudden, and usually reversible, decline in kidney function. In mice, ischemia reperfusion injury (IRI) is commonly used to model the pathophysiological features of clinical AKI. Macrophages are a unifying feature of IRI as they regulate both the initial injury response as well as the long-term outcome following resolution of injury. Initially, macrophages in the kidney take on a pro-inflammatory phenotype characterized by production of inflammatory cytokines such as CCL2 (MCP-1), IL-6, IL-1β, and TNF-α. Release of these pro-inflammatory cytokines leads to tissue damage. Following resolution of the initial injury, macrophages take on a reparative role, aiding in tissue repair and restoration of kidney function. In contrast, failure to resolve the initial injury results in prolonged inflammatory macrophage accumulation and increased kidney damage, fibrosis, and the eventual development of chronic kidney disease (CKD). Despite the extensive amount of literature that has ascribed these functions to M1/M2 macrophages, a recent paradigm shift in the macrophage field now defines macrophages based on their ontological origin, namely monocyte-derived and tissue resident macrophages. In this review, we focus on macrophage phenotype and function during IRI induced injury, repair, and transition to CKD using both the classic (M1/M2) and novel (ontological origin) definition of kidney macrophages.