Purpose: The historical underrepresentation of women in surgery has contributed to persistent gender inequalities in academic medicine. This study sought to assess any effect of gender on academic performance and research outcomes in the Master of Surgery (MS) program and examine temporal trends in gender representation. Methods: A retrospective cohort study of students that completed the MS dissertation unit at The University of Sydney between 2010 and 2021 was completed. Data included dissertation mark, dissertation publication rate, time to publication, citation count, journal impact factor and total publications within two years of dissertation completion. Outcomes were compared by student gender and student-supervisor dyads using Mann-Whitney U, Chi-Squared, and Kruskal Wallis tests. Temporal trends in student and supervisor gender were analysed using Poisson regression with robust standard errors, and binomial and negative binomial regression. Results: A total of 424 students were included (305 male, 119 female). There was no difference in dissertation mark or short-term research outcomes by student gender. Students supervised by males had higher dissertation publication rates (56% vs 30%, p < 0.001) and more publications within two years (median 1 vs 0, p=0.009) than those supervised by females. Female-female student-supervisor dyads were less likely to publish their dissertation (29%) than male-male (57%) and female-male dyads (53%) (p=0.006). Although the number of female supervisors have increased, there was no change in the number of female students, nor the proportion of female students and supervisors. Conclusion: Academic performance and research outcomes did not differ by student gender in the MS program. However, disparities associated with supervisor gender suggests ongoing structural influences on academic productivity. Persistent gender imbalances highlight the need for sustained, system-level equity initiatives across the surgical training pipeline.