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Background: Doctoral programs have consistently garnered the attention of policymakers in medical education systems due to their significant impact on the socio-economic advancement of countries. Therefore, various doctoral programs have been implemented with diverse goals. In Iran, a research doctorate program, known as PhD by Research, was introduced primarily to engage in applied research related to healthcare needs. Nevertheless, the achievement of the program's goals has been questioned. This study aimed to identify the implementation challenges of the Research Doctorate Program and its solutions in Iran. Method: This descriptive qualitative study followed the Standards for Reporting Qualitative Research: A Synthesis of Recommendations and was conducted in two steps. Firstly, the challenges of the Iranian Ph.D. by research program were identified through the perspectives of the program's students and graduates. In the second step, relevant solutions to these challenges were determined by focus groups of key informant experts. The transcripts were analyzed using qualitative content analysis. Results: Five students and six graduates were interviewed in the first step and seven experts participated in the second one. The challenges and related solutions are explored in four main themes, including: (1) admission criteria, (2) program goals and expected outcomes, (3) curricula, and (4) financial and human resources. The study showed that various dimensions of the doctoral program are not aligned with each other and how to adapt the program in these dimensions. Conclusion: The study revealed the importance of a systematic approach in defining various dimensions of doctoral programs according to program goals and provided specific solutions for defining a research doctorate program in the context of a low- and middle-income country. [ABSTRACT FROM AUTHOR]