Background: Management of HIV-infected children on a long-term basis is a challenge in resource-limited countries. The aim of this study is to evaluate the long-term outcome and identify the risk factors for mortality in a cohort of children with antiretroviral therapy (ART) in Vietnam. Patients and Methods: A retrospective cohort study was conducted in children aged 0-15 years, seen at the outpatient clinic of the Women and Children Hospital of An Giang, Vietnam, from August 2006 to May 2019. Cox proportional-hazard models were used to determine factors associated with mortality. Results: A total of 266 HIV-infected children were on ART. During 1545 child-years of follow-up (median follow-up was 5.8 years), 28 (10.5%) children died yielding a mortality rate of 1.8 death per 100 child-years. By multivariate analysis, World Health Organization clinical stage 3 or 4 (AHR; 7.86, 95% CI; 1.02-60.3, P= 0.047), tuberculosis (TB) coinfection (AHR; 6.26, 95% CI; 2.50-15.64, P= 0.001) and having severe immunosuppression before ART (AHR; 11.73, 95% CI; 1.52-90.4, P= 0.018) were independent factors for mortality in these children. Conclusion: Antiretroviral therapy has reduced mortality in HIV-infected children in resource-limited settings. Independent risk factors for mortality were advanced clinical stage (3 or 4), TB co-infection and severe immunosuppression. Early investigation and treatment of TB co-infection allow early ART initiation which may improve outcomes in our settings.