Background: Differences in physician income by gender have been described in numerous jurisdictions, but few studies have looked at a Canadian cohort with adjustment for confounders. In this study, we aimed to understand differences in fee-for-service payments to men and women physicians in Ontario. Methods: We conducted a cross-sectional analysis of all Ontario physicians who submitted claims to the Ontario Health Insurance Plan (OHIP) in 2017. For each physician, we gathered demographic information from the College of Physicians and Surgeons of Ontario registry. We compared differences in physician claims between men and women in the entire cohort and within each specialty using multivariable linear regressions, controlling for length of practice, specialty and practice location. Results: We identified a cohort of 30167 physicians who submitted claims to OHIP in 2017, including 17992 men and 12175 women. When controlling for confounding variables in a linear mixed-effects regression model, annual physician claims were $93 930 (95% confidence interval $88434 to $99431) higher for men than for women. Women claimed 74% as much as men when adjusting for covariates. This discrepancy was present in nearly all specialty categories. Men claimed more than women throughout their careers, with the greatest gap 10-15 years into practice. Interpretation: We found a gender gap in fee-for-service claims in Ontario, with women claiming less than men overall and in nearly every specialty. Further work is required to understand the root causes of the gender pay gap.