Background The proportion of women surgeons is increasing, but studies show that women in surgical residency are granted less autonomy than men. Objective We utilized the Surgical Autonomy Program (SAP), an educational framework, to evaluate gender differences in self-reported autonomy, attending-reported autonomy, and operative feedback among US neurosurgical residents. Methods The SAP tracks resident progression and guides teaching in neurosurgery. Surgeries are divided into zones of proximal development (opening, exposure, critical portion, and closure). Postoperatively, resident autonomy is rated on a 4-point scale by the resident and the attending for each part of the case, or zone. We utilized data from July 2017 to February 2024 from 8 institutions. Ordinal regression was used to evaluate the odds of self- and attending-evaluated autonomy, accounting for gender, training year, case difficulty, and institution. Differences between attending assessment and self-assessment were calculated across time. Chi-square analyses were used to measure any differences in feedback given to men and women. Results From 128 residents (32 women, 25%), 11894 cases were included. Women were granted less autonomy (OR 0.81; 95% CI 0.74-0.89; P<.001) and self-evaluated as having less autonomy (OR 0.73; 95% CI 0.67-0.80; P<.001). The odds of women operating at higher autonomy were similar to the odds of operating on a hard case compared to average difficulty (OR 0.77; 95% CI 0.71-0.84; P<.001). Men's and women's self-assessment became closer to attending assessment over time, with women improving more quickly for the critical portions of surgeries. Women residents received meaningful postoperative feedback on fewer cases (women: 74.2%, men: 80.5%; X2=31.929; P<.001). Conclusions Women operated with lower autonomy by both attending and self-assessment, but the assessment gap between genders decreased over time. Women also received less feedback from their attendings.