Background Previous studies that have focused on the challenges faced by female surgeons, such as the gender pay gap, gender biases, lower likelihood of promotion, and gender differences in the perception of discrimination against women, are reviewed. A more comprehensive understanding of explicit and implicit gender discrimination and experiences and perceptions of discrimination is needed. This study aims to determine the current prevalence and degree of gender discrimination in the Korean Surgical Society and to compare the experiences and perceptions of gender discrimination between male and female surgeons. Methods We analyzed 400 responses from a survey sent to all members of the Korean Surgical Society. This electronic survey included 16 items on experiences of gender discrimination and 17 items on perceptions of gender discrimination. We conducted χ 2 tests and binary logistic regression on the data regarding these experiences and perceptions of gender discrimination. Results Adjusted analyses found that female surgeons were more likely to experience gender discrimination than their male counterparts across all categories of discrimination. Further, adjusted analyses showed that female surgeons were more likely to confirm the presence of gender discrimination than male surgeons. Conclusion Female surgeons were more likely to experience implicit and explicit gender biases and discrimination throughout all stages of their career progression. We also discovered significant gender differences in the perception of gender discrimination, as well as the experience of it. Changing the male-dominated culture and raising awareness of gender biases and discrimination among male surgeons are crucial steps toward addressing gender discrimination in surgery.