Objectives Medical professionals are exposed to many job stressors everyday, which can lead to psychological disturbances as well as burnout syndrome. We sought to assess the level of burnout among primary care physicians (PCPs) in Oman and explore risk factors for its development. Methods We conducted a cross-sectional, analytical study among a random cluster sample of 190 PCP working in Muscat, Oman. Indices of burnout (emotional exhaustion (EE), depersonalization (DP) and personal accomplishment (PA)) were noted using the Maslach Burnout Inventory-Human Services Survey (MBI-HSS). We also used a questionnaire to obtain sociodemographic and job characteristics data. We used a binary logistic regression model and both unadjusted and adjusted odds ratios for statistical analysis. Results The prevalence of burnout in all three dimensions was 6.3%. High levels of MBI-HSS subscales were reported on EE, DP and PA with 17.8%, 38.2%, and 21.5%, respectively. Logistic regression analysis revealed that working over 40 hours per week was the most important risk factor for burnout among PCPs. Conclusions A total of 6.3% of PCPs working in urban areas in Oman suffered burnout. Long working hours was strongly associated with high occupational burnout. Solutions to eliminate or decrease the rate of burnout involve institutional changes, primarily respecting weekly working hours, and in more severe cases psychotherapy help is very important.