Objective There are significantly fewer women than men in leadership roles in health care. Previous studies have shown that, overall, male physicians earn nearly $20,000 more annually than their female physician colleagues after adjusting for confounding factors. However, there has not been a description of physician leadership compensation in relation to gender. Methods This was a successive cross‐sectional observation study design of 154 emergency departments in the United States from 5 years (2013, 2015–2018) using Association of Academic Chairs in Emergency Medicine and Academy of Administrators in Academic EM survey data. The primary variable of interest, leadership role, was attained by recoding the survey responses to assign primary job duty into four main categories: no leadership role, operations leadership, education leadership, and executive leadership. Results Overall, 8820 responses were included. Across all survey years, the mean (±SD) percentage of women in any leadership role was significantly less than men (44.5% 95% CI: 42.8, 46.2% vs. 55.3% 95% CI: 54.1, 56.5%). Women in leadership roles worked more clinical hours than men in the same position (female median = 1008, male median = 960). Women also had significantly lower salaries than men at each of the 5‐year time points that data are reported, with unadjusted mean salary differences of –$54,409 per year for executives, –$27,803 for operational leaders, and –$17,803 for education leaders. Conclusions Female physicians hold fewer leadership roles in academic emergency medicine (EM), and when they do, they work more clinical hours and are paid less than male physicians. As a specialty, EM should continue to investigate and report on gender achievement disparities as work is done to rectify the system inequalities.