We demonstrate that a bunch of RetroTransposons (TEs) are co-opted for cis-regulatory function to drive the expression of interferon-responsive genes in CD4+ T cells. A rare subset of people who control HIV spontaneously are called HIV Elite controllers have TE-mediated re-wired gene regulatory networks (GRN) activated which fight against HIV replication. Demonstrating how TEs contribute to the immune control of HIV, we open a therapeutic avenue for controlling HIV replication without usage of the anti-retroviral therapy which has considerable side effects. This study presents a useful resource and implicates TEs in the cis-regulatory control of immune genes, which is not limited to HIV but paves the way to understanding overall immune fitness. This study adds another layer to understanding genetic mechanisms of HIV control, and if further developed may comprise a useful source of biomarkers to predict viral kinetics in HIV-infected individuals.