Nipah virus (NiV) is a zoonotic pathogen that causes recurrent outbreaks with considerable implications for public health. Viruses engage host kinases to phosphorylate viral proteins, aiding replication and host disruption. Identifying NiV phosphoproteins and their host kinases is therefore critical for understanding the mechanism of infection and developing therapeutics. We performed kinase-substrate phosphomotif analysis based on prior studies and employed computational tools to identify putative phosphosites in NiV proteins and corresponding host kinases. Redundancy analysis highlighted key kinases capable of phosphorylating multiple NiV proteins and high-potential viral substrates. Integration with human–viral protein–protein interaction data revealed human kinase substrate proteins in human that interact with NiV proteins, while conservation analysis assessed phosphosites across nine NiV proteins in various strains. The functional significance of the identified and predicted viral substrates and their corresponding host kinases was further validated through in silico docking and molecular dynamics simulation (MD). Motif-based kinase-substrate analysis identified 51 human kinases predicted to target 1180 phosphorylation sites across nine NiV proteins, including key human kinases such as Eukaryotic elongation factor 2 kinase [EEF2K], Haploid germ cell-specific nuclear protein kinase [HASPIN], Mitogen-activated protein kinase 9 [MAPK9], Microtubule-associated serine/threonine-protein kinase 2 [MAST2], and Spleen tyrosine kinase [SYK], with the potential to phosphorylate multiple sites across NiV proteins. Using computational prediction tools, we identified several potential phosphorylation sites on NiV proteins, along with their corresponding candidate human kinases. In silico docking revealed interactions between EEF2K and both the NiV Fusion Glycoprotein and NiV Phosphoprotein (P), MAPK9 with the NiV Matrix Protein, and HASPIN with NiV RNA-dependent RNA polymerase. MD simulations of the EEF2K–NiV Fusion Glycoprotein complex confirmed the stability of this interaction. Leucine-rich repeat serine/threonine-protein kinase 2 [LRRK2], HASPIN, MAST2, and EEF2K were the human kinases predicted to phosphorylate experimentally validated sites on NiV nucleocapsid (N), P, and W proteins. Furthermore, through an extensive literature review, we investigated the therapeutic potential of targeting these kinases using known inhibitors and identified compounds that could potentially be repurposed as antiviral agents against NiV infection. Our findings indicate that EEF2K phosphorylates key NiV proteins at conserved phosphosites across variants, underscoring the pathogenic significance of kinases in NiV infection and their potential as therapeutic targets.