Naïve T cells are maintained in a homeostatic state to preserve a stable T cell pool with diverse T cell receptor (TCR) repertoires, ensuring preparedness for priming. However, the underlying mechanisms controlling naïve T cell homeostasis and priming remain unclear. Leveraging a machine learning-based functional genetic screen, we identified DEAD-box helicase 55 (Ddx55) as the top factor responsible for naïve T cell homeostasis. DDX55 was highly expressed in naïve T cells and suppressed enhancer- and promoter-like transposable elements (TEs) near T cell activation-associated genes. Ddx55 loss led to derepression of these TEs, resulting in TE-derived R loops and genomic instability, ultimately disrupting naïve T cell homeostasis and abolishing T cell proliferation. Mechanistically, DDX55-targeted TEs harbored myelocytomatosis oncogene (MYC)-binding motifs. DDX55 directly bound MYC and restricted its access to these TE loci, thereby preventing inappropriate TE activation in naïve T cells. Thus, naïve T cells exploit DDX55 as a vital regulator of T cell activation, ensuring their genomic stability and homeostatic maintenance.