Neurodevelopmental stimulation programmes can improve developmental outcomes. Antiretroviral therapy (ART) started soon after birth potentially limits the invasion of HIV into the central nervous system. A combination of developmental stimulation and early ART initiation may reduce developmental delays in children with perinatally acquired HIV infection. At a single site in Johannesburg, South Africa, we enrolled 36 HIV-infected neonates on ART into an intervention group (IG) participating in a yearlong home-based, neurodevelopmental stimulation programme. Bayley Scales of Infant and Toddler Development-3rd Edition (BSID-III) assessments were conducted at 12 months. Scores were compared with 24 early treated HIV-infected infants in an observational group (OG). BSID-III assessments were also conducted for older children in an OG at 24 or 36 months. Cognitive, language and motor scaled and composite scores were analysed. BSID-III scaled and composite scores were all higher in the IG apart from the gross motor scaled score (9.25 vs. 10, p = 0.1954). Receptive communication scaled score was significantly higher in the IG (10.96 vs. 9, p = 0.0331). IG composite scores were all higher than OG scores. OG children assessed at 24 or 36 months had lower composite scores in all subscales than 12-month OG scores. Early treated HIV-infected children participating in a neurodevelopmental stimulation programme achieved higher BSID-III scores at 12 months compared with early treated HIV-infected children who did not receive the programme.