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Abstract Background While triple anti-retroviral therapy (ART) has improved HIV-infected children surviving into adolescence and adulthood, these children remain vulnerable to HIV-related psychological disturbance due to both the direct HIV infection effects on the brain and indirect effects related to coping with a range of medical, psychological and social stresses associated with HIV, which makes it vital to identify their mental health needs. This study assessed the emotional and behavioural challenges of HIV perinatally infected children and adolescents with a completed disclosure process attending “ART teen club” in Malawi. Methods A cross-sectional descriptive study design was conducted to obtain quantitative descriptive descriptions of emotional and behavioural challenges among HIV-infected children and adolescents between 10 and 22 years of age. They were interviewed on their family socio-demographic characteristics, clinical characteristics as well as emotional, conduct, hyperactivity, peer and prosocial problems using the Chichewa version of the Strengths and Difficulties Questionnaire. Data were analyzed using descriptive analysis and logistic regression. Results Based on the four-band categorization of the SDQ, higher scores for total difficulties score were observed in 72.9% of the children. According to the subscales of the SDQ, results show that children had higher scores in peer problems (62.8%), emotional (68.2%), conduct (68.6%) and prosocial (57.8%) subscales while lower scores were identified in the hyperactivity (16.6%) subscale. Results show that within each level, males are having lower frequencies as compared to females. Results from multivariate binary logistic regression indicate that those with a single parent or not as well as the WHO HIV clinical stage had an impact on the mental health status of the children. Children who do not have a single parent (AOR 3.404; 95% CI:1.563–7.416, p = 0.002) had 3.404 odds of having abnormal mental health status unlike those children with a single parent and children who were in WHO HIV clinical stage 2 (AOR 2.536; 95% CI:1.005–6.395, p = 0.049) or 3 and 4 (AOR 8.459; 95% CI:1.5.820-10.544, p