Background: Female physicians face extra challenges in their career development and tend to choose salary or other forms of alternative payment plans (APP). Fee-for-service (FFS) and APP may affect the well-being of female and male physicians differently. Three measures of well-being are: levels of career satisfaction, professional equity, and daily distress. The objectives are to identify differences in the levels of career satisfaction, fulfillment-recognition equity, and daily distress of physicians by gender and payment method, and to assess interactions between these two factors. Methods: A cross-sectional study was conducted in 2011 with physicians practicing in the Saskatoon Health Region, Saskatchewan, Canada. Resident physicians were excluded from the study. Eligible physicians completed a survey, assessing levels of daily distress, fulfillment-recognition equity, and career satisfaction as dependent variables. A multivariate analysis of variance (MANOVA), using the Wilks’ Lambda criterion, was conducted to study differences among the dependent variables by remuneration method and gender. Multiple comparisons were performed as post-hoc tests. Results: Nearly half (382) of the 794 eligible physicians completed the questionnaire; 37.2% were female. Half were remunerated by FFS, a quarter by APP, and the remainder by blended forms. Career satisfaction and fulfillment-recognition equity were positively correlated to each other and daily distress was negatively correlated with both. According to the MANOVA results, the dependent variables were affected by gender but not by payment method, and there was no evidence of an interaction effect between payment method and gender. Women reported lower levels of career satisfaction (p=0.01) and fulfillment-recognition equity (p=0.01), and higher levels of daily distress (p=0.03).