We aimed to examine the differences between female and male surgeons in urology, general surgery, and gynecology by analyzing a nationwide, population-based database in Taiwan. We identified surgeons with a clinical experience of 6 − 13 years, between 1995 to 2013, from the National Health Insurance Research Database. We collected patient volume and revenue per month in outpatient and inpatient services, as well as surgical volumes per month of female and male surgeons for analysis. Student’s t-test was used to compare the differences between female and male surgeons. Female urologists and general surgeons had a significantly higher ratio of female patients. Female urologists had comparable patient numbers, revenues, and surgical volumes as male urologists. In contrast, female general surgeons had significantly lesser involvement in outpatient and inpatient care and had lower monthly revenues than males; however, female general surgeons performed more oncological surgeries per month. Female gynecologists had similar outpatient services and outpatient revenue but significantly lesser inpatient services and surgical volume per month. A gender-based gap exists among surgeons in Taiwan; this gap is narrower in urology than in general surgery and gynecology. Gender stereotypes should be reduced to ensure that patients receive the best care regardless of surgeons’ gender.