BackgroundFew studies about gender differences in job quality and job satisfaction among medical professionals have been carried out in China. So the objectives of this study were to examine whether and to what extent gender differences existed in job quality and job satisfaction of doctors in rural western China.MethodsFrom 2009 to 2011, a total of 1472 doctors from 103 selected county-level health care facilities in rural western China were recruited into the study. Information about the doctors’ demographic characteristics, job quality, and job satisfaction was collected through a designed questionnaire. Besides examining gender differences in single dimensions of job quality and job satisfaction, principal component analysis was used to construct a composite job quality index to measure the differences in the comprehensive job quality, and exploratory factor analysis was applied to evaluate the differences in the overall job satisfaction. Chi-square test was used to calculate differences between proportions, and t-test was used to compare differences between means.ResultsAmong the doctors, there were 705 males and 767 females (ratio 1:1.09). Male doctors had significantly higher monthly salaries, longer working hours, more times of night shifts per month, longer continuous working hours, and longer years of service at current facilities, and marginally significantly higher hourly wage and longer years of service in current professions. However, female doctors showed greater overall job qualities. Significant and marginally significant gender differences were only found in satisfaction with remuneration compared to workload, the chance of promotion and working environment. But female showed greater satisfaction in the overall job satisfaction and the factor including sub-aspects of working environment, remuneration compared to workload, the chance of promotion, utilization of subjective initiative, and sense of achievement.ConclusionsGender differences in job quality and job satisfaction did exist among doctors in rural western China. The participating female doctors were shown to have better job quality and greater job satisfaction.Electronic supplementary materialThe online version of this article (doi: 10.1186/s12913-017-2786-y) contains supplementary material, which is available to authorized users.