We investigated sleep quality in HIV infected individuals and its potential impact on cognitive performance and functional connectivity. Sleep quality was assessed using a self-report questionnaire, Pittsburgh Sleep Quality Index (PSQI). Cognitive performance was measured by a standard battery of neuropsychological tests assessing six cognitive domains, while functional connectivity was assessed by resting-state fMRI. We used a seed-based method to investigate the activation changes associated with the thalamus and frontoparietal network. We found a strong interaction between HIV infection and sleep quality, in the inferior temporal gyrus and the inferior parietal lobule but no deleterious effect on cognitive performance.