Shortage of healthcare workers is a global problem. It is important to clarify factors, including job stress, that influence workplace resignation and factors that cause burnout among rural physicians. The study was designed as a cross-sectional questionnaire survey. We sent questionnaires to town or village hospitals and clinics (n = 1,898) in Hokkaido, Tohoku, Shikoku, and Kyushu and Okinawa. The number of participants was 509. Of these 7.7% were female and 21.6% were < 50 years. Internal or general medicine physicians were asked about personal and job factors, job stress based on the demand-control-support model, intention to resign from current position, and burnout evaluated using the Maslach Burnout Inventory-General Survey. Overall, 10.4% of the participants intended to resign, and 21.8% was defined as burnout positive. In the multivariate logistic regression analysis, dissatisfaction with income (OR, 3.63; 95% CI, 1.63-8.10), having one’s hometown in another town or village in the same prefecture (OR, 3.53; 95% CI, 1.18-10.62) were significantly related to intention to resign, while high job control (OR, 0.72; 95% CI, 0.58-0.88) had a significantly protective effect. In the multivariate analysis, high job demand (OR, 1.48; 95% CI, 1.28-1.72) was significantly related to burnout, and high job control (OR, 0.66; 95% CI, 0.55-0.78) and high support from co-workers (OR 0.88, 95% CI, 0.78-1.00) had a significantly protective effect. Improving job stress factors, especially job control, and taking into consideration physicians’ hometown and income may be important factors to prevent resignation from a current position and burnout among Japanese rural physicians.