Advances in antiretroviral treatment improved the life expectancy of perinatally HIV-infected children. However, growing up with HIV provides challenges in daily functioning. This cross-sectional cohort study investigated the neuropsychological and psychosocial functioning of a group of perinatally HIV-infected children in the Netherlands and compared their outcomes with Dutch normative data and outcomes of a control group of uninfected siblings. The children’s functioning was assessed with internationally well-known and standardized questionnaires, using a multi-informant approach, including the perspectives of caregivers, teachers, and school-aged children. In addition, we explored the associations of socio-demographic and medical characteristics of the HIV-infected children with their neuropsychological and psychosocial functioning. Caregivers reported compromised functioning when compared to Dutch normative data for HIV-infected children in the areas of attention, sensory processing, social-emotional functioning, and health-related quality of life. Teachers reported in addition compromised executive functioning for HIV-infected children. A comparison with siblings revealed differences in executive functioning, problems with peers, and general health. The concurrent resemblance between HIV-infected children and siblings regarding problems in other domains implies that social and contextual factors may be of influence. A family-focused approach with special attention to the child’s socio-environmental context and additional attention for siblings is recommended.