The goal of this study was to understand how immune reconstitution through ART in HIV-1 infected patients affects CD4(+) recent thymic emigrants (identified as CD31(+) naïve T cells). We performed FACS analysis of CD4(+) CD31(+) naïve T cells from PBMCs in a cross-sectional age-matched cohort, including 25 healthy controls (HC), 18 untreated HIV-1 infected viremic progressors (VP), 10 untreated HIV-1 infected viral controllers (VC), and 24 HIV-1 infected immune responders (IR) following ART. Our data reveal that 37.5% of IR failed to restore their CD4(+) CD31(+) naïve T cell counts. In addition, significantly higher expressions of Ki67, CD57, and CD95 were observed in CD4(+) CD31(+) naïve T cells of both VP and IR comparing to HC and VC. The significantly elevated CD57 and CD95 expressions are observed in IR with low CD4(+) CD31(+) naïve T cell counts. Therefore, our data indicate an incomplete immune reconstitution of CD4(+) CD31(+) naïve T cells in more than one third of IR, which is associated with HIV-1 driven immunological phenotypic alterations.