The objective of the study was to evaluate the prevalence and factors associated with Burnout Syndrome (BS) in Primary Health Care (PHC) nursing professionals from the state of Bahia, Brazil. A multicentre, cross-sectional population-based study was conducted in a cluster sample among 1125 PHC Nursing professionals during the years 2017 and 2018. We used a questionnaire that included sociodemographic, labor and lifestyle variables and the Maslach Burnout Inventory scale to identify BS. The associations were evaluated using a robust Poisson regression with the hierarchical selection of the independent variables. The prevalence of BS was 18.3% and the associated factors were ethnicity (prevalence ratio (PR) = 0.62, confidence interval (CI) 95% = 0.47–0.83), residence (PR = 2.35, CI 95% = 1.79–3.09), economic situation (PR = 1.40, CI 95% = 1.06–1.86), satisfaction with current occupation (PR = 1.75, CI 95% = 1.31–2.33), (PR = 1.60, CI 95% = 1.23–2.08), rest (PR = 1.83, 95% CI = 1.41–2.37), technical resources and equipment (PR = 1.37, CI 95% = 1.06–1.77), night shift (PR = 1.49, CI 95% = 1.14–1.96), physical activity practice (PR = 1.72; CI 95% = 1.28–2.31), smoking (PR = 1.82, CI 95% = 1.35–2.45), and satisfaction with physical form (PR = 1.34, CI 95% = 1.01–179). Strategies are needed to prevent BS, with an emphasis on implementing worker health programs in the context of PHC.