Despite effective viral suppression, youth with perinatal HIV (PHIVY) often demonstrate long-term cognitive deficits. We measured grey matter cortical thickness as a measure of brain structural integrity in 11 PHIVY receiving long term cART compared to 16 age-matched controls and assessed neurocognitive performance. The PHIVY group performed significantly worse than controls. Regions of significantly thinner and thicker cortex in PHIVY were observed which may contribute to these deficits in neurocognitive function. Cortical thickness in PHIVY was correlated with current CD4 count and neurocognitive performance. Our findings suggest the potential importance of continued monitoring of PHIVY.