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Background: The COVID-19 pandemic generated uncertainty and disruption among the child and adolescent population. Multiple studies have documented a worsening of mental health following the pandemic. The main objective of this longitudinal study is to analyze the short-, medium-, and long-term evolution of the overall functioning of children and adolescents treated by a child and adolescent mental health team in the context of the COVID-19 pandemic. Methods: 420 patients aged 3 to 18 were assessed using the Global Assessment of Functioning (GAF) scale at three time points: during the lockdown, three months later, and three years later. Differences based on gender, diagnosis, and time were analyzed. Results: A significant improvement was observed in the short-term (three months) and long-term (three years) compared to the lockdown period. This improvement was maintained in all diagnostic subgroups except for mixed cases (severe mental pathology), which showed the least improvement. No significant differences were found between males and females. Conclusions: The child and adolescent population showed a greater capacity for adaptation to the lockdown than expected. Family support, decreased stress, and therapeutic intervention appear to have played an important role in improving mental health.