Objectives: Gender inequity in academic medicine persists despite increases in the number of women physicians. We sought to explore gender differences in research productivity for academic psychiatrists in Canada. Methods: In a cross-sectional study of the 3379 psychiatrists in all 17 university departments of psychiatry in Canada, research productivity, as measured by the h-index and number of publications, was compared between women and men using a negative log binomial regression model to generate relative rates (RRs), adjusted for career duration (aRR). Findings were stratified by academic rank, institution region, and institution size. A subanalysis of those with 10 or more publications was conducted as a proxy for identifying physicians on a research track. Results: Women (43% of the sample) had a lower mean (standard deviation) h-index than men (2.87 [6.49] vs. 5.31 [11.1]; aRR, 0.62; 95% confidence interval [CI], 0.54 to 0.72). Differences were significant only for junior faculty and not for associate and full professors. Comparison by number of publications followed a similar pattern (aRR, 0.46; 95% CI, 0.39 to 0.55). Among those with 10 or more publications ( n = 721), differences between men and women were smaller than in the overall cohort for both the h-index (aRR, 0.77; 95% CI, 0.68 to 0.87) and number of publications (aRR, 0.62; 95% CI, 0.53 to 0.72). Conclusions: Gender differences in research productivity at the national level in academic psychiatry in Canada support a call to adopt a more systematic approach to promoting equitable opportunities for women in research, especially in early career, to improve diversity and enhance future psychiatric research and discovery.