Calcium ion (Ca) is a widespread and primitive second messenger that regulates physiological cell functions in almost all life beings. Ca influx-induced NFAT activation is essential for T cell function and adaptive immunity. However, whether and how Ca signaling modulates T cell immunity in early vertebrates, especially in nontetrapods, remains largely unknown. To address these questions, a Nile tilapia () model was employed to investigate the regulation of ancestral T cell immunity by Ca-NFAT signaling in jawed fish. In Nile tilapia, an evolutionarily conserved Ca-NFAT signaling pathway is involved in the primary adaptive immune response during infection. Meanwhile, T cell signals trigger several events along the Ca-NFAT axis in this early vertebrate, including Ca influx, calcineurin activation, and NFAT nuclear import. More critically, suppression of Ca-NFAT signaling by the calcineurin inhibitor cyclosporine A impairs primordial T cell activation, clonal expansion, and infection clearance. Mechanistically, Nile tilapia NFAT interacts with several other transcription factors for potent gene expression, and T cells in this nontetrapod employ Cabin1 and DYRK1A to regulate NFAT nuclear import and export, respectively. To the best of our knowledge, this study is the first to demonstrate the regulatory mechanism of Ca-NFAT signaling on T cell immunity in a nontetrapod species. We suggest that modulation of T cell immunity by Ca-NFAT signaling is a primitive strategy that already existed prior to the divergence of bony fish from the tetrapod lineage. The findings of this study provide valuable perspectives for understanding the evolution of adaptive immune system.