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Background Current rates of burnout among physicians are alarming when compared to nonphysician U.S. workers, and numerous interventions have been introduced to mitigate the issue. However, no interventions have specifically targeted the 30% burnout rate among physician program directors. The complex and demanding role of program directors necessitates building relationships, solving crises, securing jobs for residents and maintaining well-being of trainees. The aim of this study is to investigate the impact of emotional intelligence (EQ) on burnout levels among program directors. Methods A cross-sectional survey was administered from May 17 to June 30, 2021 to program directors and assistant/ associate program directors at an academic medical center in south-central Pennsylvania. A self-report questionnaire was used to collect data. The survey included an open-ended question along with the Trait Emotional Intelligence Questionnaire- Short Form (TEIQue-SF), Copenhagen Burnout Inventory (CBI), and demographic questions. All data were analyzed using SAS Version 9.4. Results Of the 109 program directors and assistant/associate program directors invited in the survey, 34 (31.20%) responded. The findings indicate that there is a moderate inverse association between EQ and burnout, suggesting EQ as a protective factor against burnout. We also found that program directors who were considering leaving their position demonstrated higher levels of burnout compared to those who did not. Results from the open-ended question suggest that perceived lack of support, micromanagement, criticism, and extra duties with less payment were among the reasons program directors and associates were considering steeping down from their position. The results showed no association between EQ skills and years of practicing. Conclusions Burnout among program directors and assistant/associate program directors is not as alarming as rates of burnout among physicians-in-training. However, despite high level of EQ skills and low burnout level, nearly 43% of program directors were considering leaving their position. Nurturing EQ skills may be useful in improving retention and reducing turnover among medical leaders.