Introduction: Globally adolescents and young adults account for more than 40% of new HIV infections, and HIV-related deaths amongst adolescents increased by 50% from 2005 to 2012. Adherence to antiretroviral therapy (ART) is critical to control viral replication and preserve health; however, there is a paucity of research on adherence amongst the growing population of adolescents living with HIV/AIDS (ALHIV) in Southern Africa. We examined levels of self-reported ART adherence, barriers to adherence, and factors associated with non-adherence amongst ALHIV in Malawi. Methods: Cross-sectional study of 519 ALHIV (12-18 years) attending two large HIV clinics in central and south-eastern Malawi. Participants self-reported missed doses (past week/month), barriers to adherence, and completed questionnaires on past traumatic events/stressors, disclosure, depression, substance use, treatment self-efficacy, and social support. Biomedical data were retrieved from existing medical records. Multivariate logistic regression was performed to identify factors independently associated with self-reported ART adherence (7 day recall). Results: The mean age of participants (SD) was 14.5 (2) years and 290 (56%) were female. Of the 519 participants, 153 (30%) reported having missed ART doses within the past week, and 234 (45%) in the past month. Commonly reported barriers to adherence included forgetting (39%), travel from home (14%), busy with other things (11%), feeling depressed/overwhelmed (6%), feeling stigmatized by people outside (5%) and within the home (3%). Factors found to be independently associated with missing a dose in the past week were drinking alcohol in the past month (OR 4.96, 95% CI [1.41-17.4]), missed clinic appointment in the past 6 months (OR 2.23, 95% CI [1.43-3.49]), witnessed or experienced violence in the home (OR 1.86, 95% CI [1.08-3.21]), and poor treatment self-efficacy (OR 1.55 95% CI [1.02-2.34]). Sex and age were not associated with adherence. Conclusions: In our study, nearly half of all ALHIV reported non-adherence to ART in the past month. Violence in the home or alcohol use in the past year as well as poor treatment self-efficacy were associated with worse adherence. Sub-optimal adherence is a major issue for ALHIV and compromise treatment outcomes. Programmes specifically tailored to address those challenges most pertinent to ALHIV may help improve adherence to ART.