The reliable and sustainable energy source for supplying energy demand of rural health clinic centers (RHCC) is very important especially in Coronavirus Disease 2019 (COVID-19) epidemic. However, diesel generator due to the fuel supply and environmental challenges can’t be a sustainable source. In this regard a standalone energy system based on solar with hydrogen storage/fuel cell system is proposed to solve this issue. In the present study, five regions with different climatic conditions in Iran are considered and the layout are evaluated for the first time in RHCC with a load demand of about 10 kWh/day. HOMER software is used to optimize the size of the equipment. The results showed the capacity factor (CF) of photovoltaic panels is about 17.4–20.4%, while the CF of electrolyzers is 17–25%. The CF of fuel cell remains similar at about 36–37%. The net present value of the systems ranges 22,000–27,000$ and the levelized cost of electricity ranges 0.28–0.34 $/kWh, with the lowest (highest) values in Kerman(Gylan). The proposed system reduced the consumption of approximately 1,830 L of diesel, resulting in significant environmental benefits. The hybrid renewable energy system combining solar and hydrogen storage can be considered as sustainable solution in RHCC in Iran.