Maintenance in HIV care is important to achieve optimal personal health and HIV viral load suppression for young people living with HIV (PLWH). We assessed the relationship between incarceration and missed visits in a longitudinal data cohort of PLWH (n = 910), ages 12–24, from 14 adolescent trial network sites across the US. The time from study entry to missed visits was modeled using Cox proportional hazards models. The cohort was mostly male (78%) and African American (75%) with a median age of 22. Prior incarceration had been experienced by 39% of the cohort, with a median number of times incarcerated of 2 (IQR: 1–3). The crude and adjusted hazard ratios for missed HIV care visits comparing those with incarceration histories to those without were 1.27 (95% CI: 1.06, 1.54) and 1.53 (95% CI: 1.26, 1.86). Among those returning to care, HIV viral loads were more likely to be unsuppressed among those with incarceration history compared to those without (RR: 1.28, 95% CI: 0.95, 1.74). This association was attenuated to the null after adjustment for suppression of viral load prior to the missed visit. Young PLWH with incarceration histories are at higher risk of missing HIV care visits.