The Steppe Eagle, Aquila nipalensis Hodgson, 1833, is a migratory, endangered raptor experiencing population declines due to habitat loss and human persecution. This study aims to construct a high-quality de novo nuclear genome and complete mitochondrial genome assembly using PromethION Oxford Nanopore long-read and MGI short-read sequencing technologies. The assembled genome size was 1.21 Gb and contained 16,192 predicted protein-coding genes. Phylogenomic reconstruction based on ultraconserved elements (UCEs) robustly placed A. nipalensis within Aquilinae, with Aquila chrysaetos (Linnaeus, 1758) identified as its closest extant relative. Mitogenome-based analyses recovered congruent topology but revealed dataset-dependent differences in divergence time estimation. The most recent common ancestor of A. nipalensis and other Aquila species was estimated at approximately 3–13 million years ago, depending on dataset, whereas divergence between Aquila and Nisaetus occurred around 22 Mya. Comparative genomic analyses further identified positively selected genes associated with vesicle trafficking, secretion, and tissue development, suggesting potential adaptive signatures related to physiological performance. In conclusion, these genomic and evolutionary insights establish a foundational reference for future population genomic, adaptive, and conservation studies of this endangered raptor.