Background. Designing a payment system for healthcare workers- doctors and nurses, in particular- in the hospitals is more intricate than that for other organizations. Beyond the legal compliance, the unique features of the medical professions and nursing work environment should be considered. Due to the lack of adequate researches on payment methods for doctors and nurses in Iran, especially regarding the recent changes in "fee for services" (FFS) payment, the present study aimed to investigate the payment challenges faced by the doctors and nurses in Iranian public hospitals. Methods. Challenges were identified by interviews, and prioritized by adopting the MARCOS method. The study population included the hospital managers, healthcare payment method experts, and doctors and nurses in the public hospitals. Targeted sampling and semi-structured interviews were conducted to collect the data. In the MARCOS method, criteria determination, weighting, and scoring of the challenges were performed by five experts in the field of healthcare payment. Criteria included decreased motivation (25%), reduced productivity (15%), correction cost (40%), and implementation difficulty of the correction (20%). Calculations were performed using Excel software and determining the relevant priorities. Results. A total of 16 interviews were conducted in this study, with 10 interviews about the academic faculty and hospital managers in Isfahan University of Medical Sciences, three about the nursing experts in Tehran, and three about the Ministry of Health experts. According to MARCOS method calculations, the top 4 challenges in compensating doctors were identified as: low FFS ceiling, lack of job difficulty incentives, the inadequate impact of full-time work, and the progressive taxing. Additionally, the 2 primary challenges in compensating nurses were: irregular payment of FFS, and collective payment of FFS instead of individual payment. Conclusion. At the time of this study, Iranian public hospitals provided the doctors with individual rights, benefits, and allowances, while it provided the nurses with collective rights, benefits, and overtime pay. Although these compensation methods often posed different challenges, most of the issues were associated with the allowance payments. By prioritizing key challenges, authorities may have developed the necessary solutions for addressing the challenges as well as enhancing the satisfaction of doctors and nurses in Iranian public hospitals.