The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on the mental health and well-being of adolescents. This study aimed to investigate the development of health-related quality of life (HRQoL) and mental health among adolescents in Northern Italy by comparing cross-sectional surveys conducted in 2021 and 2022, with a particular focus on the influence of age and gender. The sample included adolescents aged 11–19 years from public schools in South Tyrol. Validated psychometric instruments were used to assess HRQoL, anxiety and depression symptoms, and psychosomatic complaints. Sociodemographic variables, COVID-19 burden, and pandemic-related factors were measured. Statistical analyses included chi-square tests, correlation coefficients, and logistic regression analyses. The results indicated that while the self-reported burden of adolescents decreased significantly in 2022 (n = 1885) compared to 2021 (n = 1760), there were no significant differences in symptoms of anxiety, depressive symptoms, low HRQoL, and increased psychosomatic complaints between the two surveys for both early and late adolescents. Females consistently had higher percentages for all outcome variables, and symptoms of anxiety increased with age in females, but not in males. Both genders experienced an increase in depressive symptoms and low HRQoL with age. The co-occurrence of mental health outcomes was observed, suggesting overlapping patterns among anxiety, depression, low HRQoL, and psychosomatic complaints. These findings underscore the intricate relationship between age, gender, and mental health outcomes among adolescents during the pandemic. It is important to recognize that late adolescents may exhibit distinct vulnerabilities and may require tailored support approaches to address their specific mental health challenges, differing from those needed for early adolescents.