Although the combination of highly active antiretroviral therapy (cART) can remarkably control human immunodeficiency virus type-1 (HIV-1) replication, it fails to cure HIV/AIDS disease. It is attributed to the incapability of cART to eliminate persistent HIV-1 contained in latent reservoirs in the central nervous system (CNS) and other tissue organs. Thus, withdrawal of cART causes rebound viral replication and resurgent of HIV/AIDS. The lack of success on non-ART approaches for elimination of HIV-1 include the targeted molecules not reaching the CNS, not adjusting well with drug-resistant mutants, or unable to eliminate all components of viral life cycle. Here, we show that our newly discovered Drug-S can effectively inhibit HIV-1 infection and persistence at the low concentration without causing any toxicity to neuroimmune cells. Our results suggest that Drug-S may have a direct effect on viral structure, prevent rebounding of HIV-1 infection, and arrest progression into acquired immunodeficiency syndrome. We also observed that Drug-S is capable of crossing the blood-brain barrier, suggesting a potential antiretroviral drug for elimination of CNS viral reservoirs and self-renewal of residual HIV-1. These results outlined the possible mechanism(s) of action of Drug-S as a novel antiretroviral drug for elimination of HIV-1 replication by interfering the virion structure.