Background Burnout is a common issue among physicians, and the rate among emergency medicine physicians (EPs) appears to be higher than those of other medical specialties. The COVID-19 pandemic presents unprecedented challenges to the medical community worldwide, but its effects on EP burnout has not yet been determined. Methods We conducted a three-stage nationwide study between July 2019 and June 2021. First, we evaluated the responses to burnout questionnaires that had been filled in by EP before the COVID-19 pandemic. We then re-sent the same questionnaires, with an addition of pandemic-specific questions. The third step involved a small group of EPs who participated in a burnout reduction workshop and re-took the questionnaires after a 3-month interval. The Maslach Burnout Inventory measured three burnout scales and a Work and Meaning Inventory predicts job satisfaction. Descriptive, univariate, and multivariate statistical tests were used to analyze the data. Results In the first stage, 240 questionnaires were sent by email to all Israeli EPs listed in emergency departments nationwide, and 84 out of 88 submitted questionnaires were completed in full before the pandemic. 393 questionnaires were sent in the second stage during the pandemic and 93 out of 101 submitted questionnaires were completed in full. Twenty EPs participated in the workshop and 13 out of 20 submitted questionnaires were completed in full. Burnout levels were high (Maslach) among EPs before the pandemic and increased during the pandemic. The feelings of personal accomplishment and work meaning—both protective factors from burnout—were significantly higher in the second (pandemic) stage. The pandemic-specific burnout factors were fear of infecting family members, lack of care centers for the physician’s children, increased workload, and insufficient logistic support. The physician-oriented intervention had no significant impact on burnout levels (p < 0.412, Friedman test). Conclusions Physician burnout is a major global problem, and it is now being aggravated by the challenges of the COVID-19 pandemic. Healthcare administrators should be alerted to pandemic-specific stress factors in order to help teams cope better and to prevent further worsening of the burnout. Further research is warranted to determine the lasting effect of the pandemic on EM physician burnout and the best means for reducing it.

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