Aim: The objective of this study was to determine the prevalence of burnout syndrome and associated factors among family physicians before and after family medicine system (FMS). Materials and Method: The first part of the study was conducted in 2008 (pre-FMS) and the second part in 2012 (post-FMS). Physician's burnout was investigated by using the Maslach Burnout Inventory (MBI). In total, 139 physicians had been participating pre-FMS and 246 physician's post-FMS. Results: The mean pre-FMS emotional exhaustion score was 15.7 5.8, increasing significantly to 17.14 7.5 post-FMS (P = 0.045). Mean pre-FMS and post-FMS depersonalization and reduced personal accomplishment scores were similar (P 0.05). Age was negatively correlated with depersonalization in this study (P = 0.012) and positively correlated with personal accomplishment (P = 0.001). The primary care physicians in the post-FMS period were older, female physicians had a greater preference for primary care, and the levels of married doctors were higher. In addition, a higher level of physicians also owned their own home and cars compared to the pre-FMS period. A negative correlation has been reported between physicians' burnout levels and home or car ownership in the present study. Conclusion: Our findings suggest that physicians working under the family medicine system, a new primary care model, are at greater risk of emotional exhaustion, but that no change has occurred in terms of personal accomplishment or depersonalization, despite this new system.