Psychological impact is one of the direct and indirect consequences of HIV and AIDS on children. A national survey applying a cross-sectional comparative design was conducted among children aged 4-16 years with parental HIV infection and age-group matched neighbourhood peers without parental HIV infection to identify and compare their psychological behaviours and determinants. A multistage sampling method was used. Face-to-face interviews were conducted with parents/guardians of the children to obtain family characteristics and children’s psychological behaviours using the modified Strengths and Difficulties Questionnaire. Factor analysis identified three domains of psychological behaviours, namely social, emotional and conduct behaviours. Comparison of these behaviours was done using Chi-squared test with Rao-Scott adjustment. Determinants of these behaviours were identified using survey-weighted logistic regression adjusted for socio-demographic variables. A total of 1280 children with parental HIV infection and 1279 neighbourhood peers participated in the study. Social conditions of the two groups differed in terms of family displacement (24.6% vs. 8.9%, p < 0.001), family dispersion (12.4% vs. 3.7%, p < 0.001), and child displacement (10.3% vs. 3.5%, p < 0.001). Emotional behaviour was significantly different between the two groups (31.3% vs. 24.0%, p < 0.01) but no difference in social or conduct behaviours was evident. Children from extended families (adjusted odds ratio (AOR): 1.34, 95% CI: 1.07-1.67), females (AOR: 1.37, 95% CI: 1.07-1.75), orphans (AOR: 1.62, 95% CI: 1.29-2.05) and children who experienced family displacement (AOR: 1.38, 95% CI: 1.11-1.72) were more likely to have abnormal emotional behaviour. Children from extended families (AOR: 0.77, 95% CI: 0.62-0.97) had less chance of having abnormal conduct behaviour. In contrast, preschool (AOR: 2.73, 95% CI: 1.92-3.87) and out-of-school children (AOR: 1.47, 95% CI: 1.01-2.27) were more likely to have abnormal conduct behaviour. Development of long-term strategies for reducing the risk of behavioural problems among children with parental HIV infection is suggested.