The COVID-19 pandemic abruptly disrupted the lives of 1.7 million children and adolescents in Austria. School closures, social distancing, and limited leisure activities substantially affected daily routines and emotional well-being. This study examined age- and gender-related differences in anxiety and depression following COVID-19 infection in Austrian youth. A cross-sectional online survey conducted between March and October 2021 included 1495 families with children aged 4–18 years who had been infected during the early phase of the pandemic. Parents completed the DISYPS-III screening for anxiety and depression. Depression scores were elevated in younger children aged 4–10 years. Boys aged 11–13 years showed slightly higher anxiety and depression levels than girls. School-related stress was associated with poorer mental health outcomes, and longer quarantine duration correlated with higher symptom levels. The findings highlight age-specific vulnerabilities and the strong impact of school-related stress on mental health during public health crises.