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Youth living with HIV (YLWH) are less likely than older adults to achieve and sustain viral suppression. While treatment guidelines recommend decreased viral load (VL) monitoring in individuals with well-controlled HIV, the appropriateness of this strategy for adolescents is unknown. We conducted a retrospective cohort study to describe longitudinal viral suppression and identify incidence of, and risk factors for, virologic failure among YLWH at a US adolescent HIV clinic from 2002 to 2015. We utilized Cox proportional hazards modeling to compare hazard ratios (HRs) for virologic failure stratified by baseline characteristics. Study participants (n = 365) were predominately African American (87%) and cisgender men and transgender women who have sex with men (80%) and the majority (79%) entered care from 2002 to 2012. Of antiretroviral therapy (ART)-treated participants (n = 201), 88% achieved viral suppression, with 29% subsequently developing virologic failure at a median 12.0 months [interquartile range (IQR) 6.9–22.4] after suppression. The cohort incidence rate of virologic failure was 200 (confidence interval [95% CI]: 151–264) per 1000 person years (PY), with a rate after ≥2 years sustained suppression of 113 (95% CI: 57–227) per 1000 PY. After adjusting for time to ART initiation, initial regimen class, and year of cohort entry, cisgender women had increased hazards of virologic failure (HR 3.2 95% CI: 1.3–7.9, p = 0.01). In conclusion, youth remained at high risk of virologic failure throughout their treatment course, with higher hazards of virologic failure among cisgender women compared with other youth. Maintaining frequent VL monitoring in YLWH may be warranted, even after prolonged viral suppression.