The COVID-19 pandemic has deeply impacted several aspects of the lives of children and adolescents. We analyzed the trends of psychiatric disorders in the emergency room. The analysis comprised the pre-pandemic (2018–2019) and the pandemic years (2020–2021). We conducted a retrospective observational epidemiological study that compared admissions during the two periods on a sample of 1311 patients aged between 4 and 18, focusing on new admissions vs. relapse, demographic variables, lockdown severity, presentation of psychiatric symptoms, diagnosis, severity, and outcome. Over the two-year pandemic period, we observed a 33% decrease in admissions to the emergency room for non-psychiatric disorders and a 200% increase in admissions for psychiatric emergencies. This increase is concentrated in periods with fewer restrictions and in the second year of the pandemic. We also observed a greater impact of psychiatric disorders on female patients, a greater severity of psychiatric disorders, a change in diagnoses associated with the presentation of symptoms, and an increase in hospitalizations. The children’s psychiatric emergency service faced an “emergency within the emergency”. In the future, it will be necessary to continue the follow-up of these patients, strengthen the field of study of gender psychiatry, and intensify our efforts towards prevention.