The COVID-19 pandemic and containment efforts seem to be particularly challenging for adolescents. This study assessed mental health in 14- to 20-year-old high school students 1.5 years after the beginning of the COVID-19 pandemic in Austria. A cross-sectional survey was carried out from 14th September 2021 to 14th November 2021. Well-being (WHO-5), depressive symptoms (PHQ-9), anxiety symptoms (GAD-7) and sleep quality (ISI) were assessed. A total of 1505 adolescents participated (77.9% girls). The cut-off for clinically relevant depressive symptoms (i.e., PHQ-9 score, ≥11) was exceeded by 61.9% girls and 38.1% boys and 49.3% girls and 28.8% boys had clinically relevant anxiety symptoms (i.e., GAD-7 score, ≥11). Clinically relevant moderate insomnia (i.e., ISI score, ≥15) was reported by 27.5% girls and 16.7% boys. The prevalence of suicidal ideation (item 9 of the PHQ-9) within the last 2 weeks was 46.8% in girls and 32.0% in boys. These data collected in autumn 2021 (at the start of the second semester of reopened schools; t2) were compared to data collected in February 2021 (one semester after almost exclusively remote schooling; t1). A matched pairs analysis according to age, gender, region, school type and migration background resulted in a total sample size of N = 2514 adolescents (70.1% females). Results showed small reduction in mental health (i.e., well-being, depressive symptoms, insomnia, suicidal ideation) in girls at t2 compared to t1, and an increase in suicidal thoughts in boys (all p-values <0.05). Results suggest that mental health burden in adolescents remained high 1.5 years after the start of the COVID-19 pandemic and highlight the need to implement timely psychological support.