BackgroundHuman resources are vital for delivering health services, and health systems cannot function effectively without sufficient numbers of skilled, motivated, and well-supported health workers. Job satisfaction of health workers is important for motivation and efficiency, as higher job satisfaction improves both employee performance and patient satisfaction. Even though several studies have addressed job satisfaction among healthcare professionals in different part of the world, there are relatively few studies on healthcare professionals’ job satisfaction in Ethiopia.MethodsA facility-based cross-sectional study was conducted among health professionals working in health centers in April 2015 using self-administered structured questionnaires. All 322 health professionals working in 23 randomly selected public health centers were included. Factor scores were computed for the identified items by varimax rotation to represent satisfaction. Multivariate linear regression analysis was performed, and the effect of independent variables on the regression factor score quantified.ResultsThree hundred eight respondents participated with a response rate of 95.56%. The overall level of job satisfaction was 41.46%. Compensation (benefits) (beta 0.448 [95% CI 0.341 to 0.554]), recognition by management (beta 0.132 [95% CI 0.035 to 0.228]), and opportunity for development (beta 0.123 [95% CI 0.020 to 0.226]) were associated with job satisfaction. A unit increase in salary and incentives and recognition by management scores resulted in 0.459 (95% CI 0.356 to 0.561) and 0.156 (95% CI 0.065 to 0.247) unit increases in job satisfaction scores, respectively.ConclusionsThe overall level of job satisfaction in health professionals was low. Salary and incentives, recognition by management, developmental opportunities, and patient appreciation were strong predictors of job satisfaction.Electronic supplementary materialThe online version of this article (doi:10.1186/s12960-017-0206-3) contains supplementary material, which is available to authorized users.