The COVID-19 pandemic has provided challenges to all healthcare workers. While the brunt of treating COVID-19 patients fell upon adult providers, pediatricians also experienced significant stressors and disruptions. Academic pediatricians and trainees (fellows and residents) were redeployed to manage adult patients in hospitalist and intensive care settings and/or had major changes to their clinical schedules. In this study, we aimed to describe levels of self-reported depression, anxiety, and burnout in pediatric physicians following the initial wave of the pandemic at the largest integrated health system in New York State. A cross-sectional study was conducted among pediatric physicians who cared for patients during the COVID-19 pandemic within the Northwell Health System as part of the Northwell Wellbeing Registry, a longitudinal registry assessing the psychological impact of COVID-19 on healthcare providers. A total of 99 pediatric physician respondents were included in this study; 72% of whom were attendings, 28% of whom were trainees. Compared to attendings, trainees reported significantly higher proportions of burnout–emotional exhaustion (p = 0.0007) and burnout–depersonalization (p = 0.0011) on the Abbreviated Maslach Burnout Inventory. There was not a similar trend in probable depression or probable anxiety using the Patient Health Questionnaire. In a multivariable logistic regression model, being a trainee was significantly associated with increased odds of burnout–emotional exhaustion (OR 5.94, 95% Confidence Interval: 1.85–19.02). These findings suggest that fellows and residents were a vulnerable population during the COVID-19 pandemic. Training programs should pay special attention to their trainees during times of crisis, and future studies can help to identify protective factors to reduce the risk of burnout during these times.