BACKGROUND: The aim of this study was to determine the prevalence of neurological disorders and their associated correlates and relations with clinical and behavioural problems among children and adolescents with HIV/AIDS (CA-HIV). METHODS: This study involved a sample of 1070 CA-HIV/caregiver dyads who were evaluated at their 6-month follow-up visit as part of their participation in the longitudinal study, 'Mental health among HIV infected CHildren and Adolescents in KAmpala and Masaka, Uganda (the CHAKA study)'. Participants completed an extensive battery of measures that included a standardized DSM-5- referenced rating scale, the parent version (5-18 years) of the Child and Adolescent Symptom Inventory-5 (CASI-5). Using logistic regression, we estimated the prevalence of neurological disorders and characterised their associations with negative clinical and behavioural factors. RESULTS: The overall prevalence of at least one neurological disorders was 18.5% (n = 198; 95% CI, 16.2-20.8). Enuresis / encopresis was the most common (10%), followed by motor/vocal tics (5.3%); probable epilepsy was the least prevalent (4%). Correlates associated with neurological disorders were in two domains: socio-demographic factors (age, ethnicity and staying in rural areas) and HIV-related factors (baseline viral load suppression). Enuresis/encopresis was associated with psychiatric comorbidity. Neurological disorders were associated with earlier onset of sexual intercourse (adjusted OR 4.06, 95% CI 1.26-13.1, P = 0.02). CONCLUSIONS: Neurological disorders impact lives of many children and adolescents with HIV/AIDS. There is an urgent need to integrate the delivery of mental and neurological health services into routine clinical care for children and adolescents with HIV/AIDS in sub-Saharan Africa.