The goal of this study was to examine the influence of the COVID-19 pandemic, including public health measures (mitigation and containment efforts), on new onset mental health diagnoses by age group. This study was a longitudinal retrospective cohort study. Data on new mental health diagnoses were extracted from the University of California Health System Electronic Health Records (EHR) that contained five academic health centers in California. Data were examined for identical timeframes before the COVID-19 pandemic (historical control cohort) and following the start of the pandemic (case cohort). Paired t-tests were used to test for differences in the number of new mental health diagnoses by age group. A two-way ANOVA was used to test for between group differences. The largest increase in mental health diagnoses (overall) was observed in the 26-35-year-old age group (p < 0.001) and for the following mental health diagnoses: anxiety, bipolar, depression, mood disturbance, and psychosis. Study findings may inform post-pandemic recovery efforts and pandemic preparedness strategies for future public health emergencies. Specifically, findings may guide the deployment of mental health screening, universal mental health interventions, and resource allocation for mental health to best support at risk groups during times of high vulnerability.