The CNS remains vulnerable to HIV-induced damage despite highly active antiretroviral therapy (HAART). Using a rigorous simian immunodeficiency virus (SIV) macaque model of HAART that combines three classes of antiretroviral drugs (a protease inhibitor, a reverse transcriptase inhibitor, and an integrase inhibitor), we examined immune responses and virus replication in the plasma and cerebrospinal fluid (CSF) following HAART initiation during acute infection (4 days postinoculation (p.i.)). HAART-treated macaques did not experience the level of acute CD4+ and CD8+ T cell and NK cell count suppression in the peripheral blood normally observed during acute infection. Initiation of HAART produced a rapid four-log decline in viral load in plasma and a slower two-log decline of viral RNA in the CSF over the subsequent 17 days of infection. Despite a dramatic reduction of viral RNA levels in the brain at 21 days p.i., viral DNA levels were not different between the two groups. Expression of most cytokine mRNA in brain of HAART-treated macaques did not significantly differ from untreated controls. Expression of the IFN responsive gene MxA was significantly reduced in the brain of HAART-treated macaques, suggesting control of hyperactive immune responses. Control of virus replication likely was enhanced by significant increases in CD4+ and CD8+ T cell trafficking in the brain of infected animals on HAART therapy and the concomitant increase in levels of IFNγ. Collectively, these data indicate preserved innate and adaptive immune activity in the brain following HAART initiation during acute SIV infection in this macaque model, suggesting profound benefits following acute treatment of SIV.