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Abstract Background This study aimed to reflect on scientific experts’ and executive stakeholders’ opinions on how charitable organizations can participate in the health care system properly and cope with problems, challenges, strategies, and executive requirements at three major levels of prevention, treatment, and rehabilitation. Methods A total number of 20 semi-structured interviews were conducted with scientific experts and executive stakeholders, selected for this qualitative study, based on an interview guide. Using the purposeful sampling method, we selected scientific experts with 5 years of experience in the health care system and executive stakeholders who had 5 years of experience in charitable activities. We applied a framework method for data analysis, and the main themes were extracted through MAXQDA software. Results Our findings revealed that charitable organizations at the major levels of the health care system, i.e., prevention, treatment, and rehabilitation, possessed the necessary capacities to provide services effectively. Nevertheless, charities encountered some problems, e.g., financial instability, non-recognition of donors’ legal status, non-involvement in policy-making, inadequate cooperation from other agencies, absence of transparent programs and goals, together with weaknesses in advertising and attracting donations. It was noted that the government should take more operational steps towards supporting such organizations, e.g., by granting special facilities and exemptions, engaging charities in policy-making and training processes, and empowering them in terms of the production of resources. Charitable organizations are also recommended to establish external communications with other bodies such as municipalities, secretaries of state, governorate offices, welfare organizations, relief committees, and medical sciences universities. Conclusions Charitable organizations have the potentials to provide health care services at prevention, treatment, and rehabilitation levels. Thus, it is of utmost importance to adopt strategies such as creating sustainable funding sources, training charity managers with a wide variety of scientific management techniques, and implementing their intellectual capacities in legislative and planning processes.