Background In Thailand, the shortage and maldistribution of physicians in the public sector is a critical public health problem. The aims of this study are to describe the retention situation of new physicians and to determine factors associated with new physicians’ decision to serve in public facilities. Methods Data of new physicians from the Human Resource Office of the Permanent Secretary System (HROPS) were analysed in order to describe the retention situation of new physicians. A retrospective cohort study was conducted to determine factors associated with new physicians’ decision to remain in public service. The data were collected between Oct 2021 and Jan 2022. Cox regression was performed. Results According to the HROPS database, most new physicians remained in hospitals affiliated to the Office of the Permanent Secretary (OPS) of the Ministry of Public Health (MOPH) (83.5%). Among the physicians resigning from MOPH hospitals, 80.6% resigned due to career factors. From a retrospective cohort study, physicians in the special recruitment track had the lowest incidence rate of resigning. In terms of satisfaction, most physicians were least satisfied with salary levels and workload. The majority of physicians felt satisfied with being close to their families. The Cox regression revealed that physicians graduating from private medical schools or from abroad had a higher risk of leaving public facilities. Conclusion To lessen the burden of physician shortage and maldistribution, the proportion of students recruited in the special track should be enhanced. High workload and inappropriate income should be addressed. Allocating new physicians to work in their hometown is recommended.