Background: Research has not explicitly explored differences between male and female microvascular head and neck (MHN) surgeon burnout, which should be identified and addressed to ensure career satisfaction and longevity. Objective: To measure and compare the prevalence of burnout among male versus female MHN surgeons. Methods: A prospective questionnaire based on the Maslach Burnout Inventory (MBI) was distributed through a web-based survey to the American Association of Facial Plastic and Reconstructive Surgeons and American Head and Neck Society in 2021 and 2022. Additional variables collected included demographics, relationship and parental status, academic rank, annual salary, and COVID-19-related questions. Results: One hundred thirteen surveys were collected. Twenty-nine (25.7%) were women and all completed MHN surgery fellowships. Women trended toward more emotional exhaustion than men (2.8 mean MBI vs. 2.3 mean MBI) but reported similar personal achievement (4.8 mean MBI vs. 4.9 mean MBI). Men experienced less workplace sexual harassment (p < 0.001). Women experienced more burnout (69% vs. 39%, p = 0.006) during the COVID-19 pandemic. Conclusion: Female MHN surgeons reported in this survey to experience more workplace sexual harassment and higher COVID-19-related burnout than their male counterparts.