Objective: To compare gender compositions in the leadership of the top 25 medical schools in North America with the leadership of their affiliated university senior leadership and other faculties. Materials and Methods: This retrospective cross-sectional observational study used publicly available gender data from 2018 to 2019 of universities drawn from the U.S. News Best Global Universities for Clinical Medicine Ranking report. Gender compositions in eight leadership tiers from senior leadership to medical school department directors were analyzed. Data analysis included gender compositions by leadership tier and faculty. Results: Male representation is greater at higher leadership tiers, with the largest imbalance being at the level of medical school department heads. The faculty of medicine has more men in leadership positions than the average of the other faculties (p = 0.02), though similar to schools of engineering, business, dentistry, and pharmacy. Across the eight leadership tiers, a significant trend exists between tier and proportions, indicating that male representation was greater at higher tiers (p < 0.001). No correlation was found between a university's leadership gender composition and its ranking. Conclusion: The under-representation of women is greater in medical school leadership than the leadership of their affiliated universities. The faculty of medicine has greater male over-representation than the average of the other faculties.