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The COVID-19 pandemic notably altered adolescent substance use during the initial stage (Spring 2020) of the pandemic. The purpose of this longitudinal study is to examine trajectories of adolescent substance use across the pandemic and subsequent periods of stay-at-home orders and re-opening efforts. We further examined differences as a function of current high school student versus graduate status. Adolescents (n = 1068, 14–18 years, Mage = 16.95 years and 76.7% female at T1) completed 4 different self-report surveys, starting during the first stay-at-home order and ending approximately 14 months later. Negative binomial hurdle models predicted: (1) the likelihood of no substance use and (2) frequency of days of substance use. As hypothesized, results demonstrated significant increases in adolescents’ likelihood of alcohol use, binge drinking, and cannabis use once initial stay-at-home orders were lifted, yet few changes occurred as a result of a second stay-at-home order, with rates never lowering again to that of the first lockdown. Further, graduates (and particularly those who transitioned out of high school during the study) demonstrated a greater likelihood and frequency of substance use and were more stable in their trajectories across periods of stay-at-home orders than current high school students. Unexpectedly, however, there was a strong increase in current high school students’ likelihood of e-cigarette use and a significant linear increase in participants’ frequency of e-cigarette use over the study. Results suggest adolescent substance use, and in particular, e-cigarette use among current high school students, may be of increasing concern as the pandemic evolves.