Background. Primary health care physicians are at high risk of burnout. In addition, with the current conditions, they can have an effort-reward imbalance. However, studies on this topic concerning public primary health care (Puskesmas) physicians in Indonesia are still limited. Objectives. To assess whether the effort-reward imbalance among Puskesmas physicians is associated with two main burnout dimensions: emotional exhaustion and depersonalisation. Material and methods. This cross-sectional study surveyed physicians working in Puskesmas in Indonesia using the short version of the Effort-Reward Imbalance Questionnaire and Maslach Burnout Inventory-Human Services Survey questionnaires. Results. Of 226 physicians, 45.6% perceived high effort and low reward. A perceived effort-reward imbalance was higher among those working more than 40 hours weekly in work shifts and in urban areas. Significant predictors of emotional exhaustion included effortreward ratio (β = 0.426; p < 0.001), overcommitment (β = 0.393; p < 0.001) and working period at Puskesmas (β = -0.122; p = 0.038). Predictors of depersonalisation include effort-reward ratio (β = 0.257; p -= 0.001), overcommitment (β = 0.170; p = 0.024), and night shift (β = 0.134; p -= 0.042). Conclusions. The effort-reward imbalance is significantly associated with emotional exhaustion and depersonalization. Therefore, it is important to set up the maximum working hours, balanced shift work arrangements, and standardized rewards for Puskesmas physicians.