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Abstract Background Despite increasing popularity among health organizations of pay for performance (P4P) for the provision of comprehensive care for chronic non-communicable diseases, evidence of its effectiveness in improving health system outcomes is weak. An important void in the evidence base is whether there are gendered differences in P4P uptake and in related outcomes amenable to healthcare improvement. This study assesses the gender-specific effects of P4P among family physicians on diabetes healthcare costs in a context of universal health coverage. Methods We use population-based linked longitudinal administrative datasets on chronic disease cases, physician billings, hospital discharge abstracts, and physician and resident registries in the province of New Brunswick, Canada. We estimate the effects of introduction of a P4P scheme on excess public healthcare costs among cohorts of adult diabetes patients using propensity score-adjusted difference-in-differences regressions stratified by physician’s gender. Results We observed greater male physician uptake of incentive payments, seemingly exacerbating gender gaps in professional remuneration. Regression results indicated P4P did not lead to improved outcomes in terms of preventing hospitalization costs among patients, only measurable increases in compensation for both the male and female physician workforce. Conclusions While P4P was not attributed in this study to reduced hospital burden and enhanced sustainability of healthcare financing, incentive payments were found to be related to earning gaps by physician’s gender. Decision-makers should consider that benefits of P4P be monitored not only for patient metrics but also for provider metrics in terms of gender equality especially given feminization of primary care medical workforces.