Viral suppression with antiretroviral therapy (ART) is a critical component of UNAIDS objectives to end the HIV epidemic. Youth living with HIV (YLH) have worse viral suppression rates than adults. The aim of this study was to identify risk factors for viral non-suppression among YLH in Nigeria. A secondary analysis of enrollment data from the iCARE Nigeria study, collected April-October 2021 for 541 YLH comprised demographic, psychosocial, behavioral, clinical variables, and viral load quantification. Viral non-suppression was defined as viral load ≥ 200 copies/mL. Generalized linear models using Akaike information criterion for selection of indicator variables in a stepwise approach were used to determine the risk factors for viral non-suppression. The final analytic sample was 491 and the proportion of non-suppressed participants at baseline was 40%. In the final model, substance use (other than alcohol, tobacco and/or cannabis) (aOR = 3.20 [95% CI: 1.05, 10.34]), missed medication doses (aOR = 1.09 [95% CI: 1.04, 1.15]), and a higher number of self-reported medication barriers (e.g., forgot, busy, change in routine) (aOR = 1.08 [95% CI: 1.00, 1.16]) were associated with a higher likelihood of viral non-suppression. Being prescribed a first-line regimen (aOR = 0.28 [95% CI: 0.17, 0.44]), disclosure to at least one brother (aOR = 0.64 [95% CI: 0.42, 0.97]), and higher treatment outcome expectancies (e.g., taking medication will improve health) (aOR = 0.81 [95% CI: 0.66, 0.98]), were all associated with a lower likelihood of viral non-suppression. Viral non-suppression among YLH in Nigeria is associated with psychosocial and behavioral factors, including missed doses, medication barriers, treatment outcome expectancies, and disclosure, that are potential targets for intervention to achieve ART goals.