Gender disparities are prevalent in the neurosurgical field, particularly for female trainees, despite the growing demand for neurosurgeons. The situation is bleaker in low-and middle-income countries, where gender disparities among neurosurgical trainees have not been evaluated. We aimed to gauge the gender differences in opportunities and perceptions of neurosurgery training in Pakistan by comparing responses between males and females. A nationwide web-based survey was conducted in Pakistan, covering 22 College of Physicians and Surgeons of Pakistan (CPSP) accredited neurosurgery training programs. Convenience sampling was used with a pilot-tested questionnaire. Data analysis was performed using SPSS version 26. A total of 120 trainees participated in our survey. The mean age of the participants was 30.4 ± 4.1 years, with 29.2% females and 70.8% males. Concerns about gender equity were more among females (34.3%) than males (27.1%). Poor work-life balance was reported by more females (34.3%) than males (30.6%). Burnout due to working hours was strongly agreed by more females (54.3%) than males (35.3%). More females (40%) acknowledged sufficient mentorship opportunities versus males (25%). Female respondents (65.7%) worked 50-100 hours per week, less than males (69.4%). Satisfaction with surgical exposure was lower among females (2.9%) compared to males (18.8%). More females reported access to teaching courses (82.9% vs. 77.6% males) and neurosurgical conferences (85.7% vs. 80.0% males), cadaver workshops (17.1% vs. 12.9% males), morbidity and mortality meetings (88.6% vs. 82.4% males), case-based sessions (82.9% vs. 75.3% males), and radiology discussions (82.9% vs. 74.1% males). Our study highlights substantial gender gaps in neurosurgical training, concerns over working hours, burnout, mentorship, work-life balance, and gender equity. These findings underscore the necessity for interventions to rectify these disparities and foster gender equity in neurosurgical training.