We tested the hypothesis that vitamin D deficiency (VDD) is associated with higher developmental disorder probability in 604 children with perinatal HIV infection (CPHIV,n= 199), HIV exposed and uninfected (CHEU,n= 196), and HIV unexposed uninfected (CHUU,n= 201). Children at 6–18 years old and their adult caregivers were assessed at enrollment, 6, and 12-month follow-ups. Serum 25-hydroxyvitamin-D (25OHD) levels in children quantified per the NHANES protocol were used to define VD categories as VDD (25OHD < 20 ng/mL), VD insufficient (VDI, 20 ≤ 25OHD ≤ 25 ng/mL), and VD sufficient (VDS = reference group if 25OHD > 25 ng/mL). Perinatal HIV status per DNA polymerase chain reaction/HIV rapid diagnostic tests included: CPHIV, CHEU, and CHUU. Developmental stage was defined as pre-adolescent (age < 11) vs. adolescent (age ≥ 11) years. Caregiver responses to standardized questions from Behavioral Assessment System for Children, Third Edition (BASC-3), were used to calculate probability scores for four disorders, namely: autism (ASD), attention deficit & hyperactivity (ADHD), emotional behavioral disorder (EBD), functional impairment (FI), and resiliency at 0, 6 and 12 months. Multivariable longitudinal models estimated VD-associated standardized mean difference (SMD) and corresponding 95% confidence intervals (95% CI) in respective probability scores in Statistical Analysis Software (v.9.4). Baseline VDD vs. VDS predicted higher probability scores of moderate clinical importance for ASD, ADHD, EBD, and higher FI among pre-adolescents (SMD = 0.32 to 0.40, 95% CI: 0.00 to 0.74). VDD was not associated with resiliency or any developmental disorders among adolescents. VDD predicted higher developmental disorder and FI scores over 12 months in a developmental stage-dependent manner. This relationship requires further understanding to appropriately target future interventions.