Introduction: Although gender discrimination and bias (GD/bias) experienced by female surgeons in the developed world has received much attention, GD/bias in lower-middle-income countries like Pakistan remains unexplored. Thus, our study explores how GD/bias is perceived and reported by surgeons in Pakistan. Method: A single-center cross-sectional anonymous online survey was sent to all surgeons practicing/training at a tertiary care hospital in Pakistan. The survey explored the frequency, source and impact of GD/bias among surgeons. Results: 98/194 surgeons (52.4%) responded to the survey, of which 68.4% were males and 66.3% were trainees. Only 19.4% of women surgeons reported ‘significant’ frequency of GD/bias during residency. A higher percentage of women reported ‘insignificant’ frequency of GD/bias during residency, as compared to males (61.3% vs. 32.8%; p = 0.004). However, more women surgeons reported facing GD/bias in various aspects of their career/training, including differences in mentorship (80.6% vs. 26.9%; p < 0.005) and differences in operating room opportunities (77.4% vs. 32.8%; p < 0.005). The source was most frequently reported to be co-residents of the opposite gender. Additionally, a high percentage of female surgeons reported that their experience of GD/bias had had a significant negative impact on their career/training progression, respect/value in the surgical team, job satisfaction and selection of specialty. Conclusion: Although GD/bias has widespread impacts on the training/career of female surgeons in Pakistan, most females fail to recognize this GD/bias as “significant”. Our results highlight a worrying lack of recognition of GD/bias by female surgeons, representing a major barrier to gender equity in surgery in Pakistan and emphasizing the need for future research.