BACKGROUND: Children and adolescents with HIV/AIDS are more likely to have emotional and behavioral problems than the general population. This can result in a continuing negative influence on the quality of life, school performance, immunity and co-morbidity of children and adolescents with HIV/AIDS. OBJECTIVE: To assess the prevalence and associated factors of Emotional and Behavioral Problems among children and adolescents on Highly Active Anti-Retroviral Therapy in the public hospitals of West Gojjam Zone, Amhara regional state of Ethiopia. METHODS: An institutional based cross sectional study was conducted by screening 411 children and adolescents for emotional and behavioral problems using Pediatric Symptomatology Check List (PSCL). Systematic random sampling technique was used to select the study participants. Data analysis was done using SPSS version 23. Bivariable and multivariable logistic regression analysis were fitted to identify factors associated with Emotional and Behavioral Problems. Odds ratio (OR) with 95% confidence interval (CI) was computed to determine the level of significance. RESULT: Out of the total 411 participants, 43.6% were screened positive for Emotional and Behavioral Problems. Lower age (AOR = 5.33, 95%CI: 2.56-11.04), having non-kin care giver (AOR = 4.64, 95%CI: 1.20-17.90), parental loss (AOR = 2.15, 95%CI: 1.03-4.49), non self -disclosure of HIV sero status (AOR = 1.99, 95% CI: 1.16-3.41) and having distressed care giver (AOR = 1.64, 95%CI: 1.04-2.57) had statistically significant association with EBPs. CONCLUSION: The prevalence of Emotional and Behavioral Problems is high among children and adolescents on HAART. Lower age, care giver's mental distress, non-self disclosure status, having non-kin care giver and parental loss were variables significantly associated with EBPs. This demonstrates a need for the integration of Mental Health and Psycho Social Support (MHPSS) service with HIV/AIDS care.