COVID-19 is a highly prevalent disease that has led to numerous predicaments for healthcare systems worldwide. Owing to the significant influx of patients and limited resources of health services, there have been several limitations associated with patients' hospitalization. These limitations can cause an increment in the COVID-19-related mortality due to the lack of appropriate medical services. They can also elevate the risk of infection in the rest of the population. The present study aims to investigate a two-phase approach to designing a supply chain network for hospitalizing patients in the existing and temporary hospitals, efficiently distributing medications and medical items needed by patients, and managing the waste created in hospitals. Since the number of future patients is uncertain, in the first phase, trained Artificial Neural Networks with historical data forecast the number of patients in future periods and generate scenarios. Through the use of the K-Means method, these scenarios are reduced. In the second phase, a multi-objective, multi-period, data-driven two-stage stochastic programming is developed using the acquired scenarios in the previous phase concerning the uncertainty and disruption in facilities. The objectives of the proposed model include maximizing the minimum allocation-to-demand ratio, minimizing the total risk of disease spread, and minimizing the total transportation time. Furthermore, a real case study is investigated in Tehran, the capital of Iran. The results showed that the areas with the highest population density and no facilities near them have been selected for the location of temporary facilities. Among temporary facilities, temporary hospitals can allocate up to 2.6% of the total demand, which puts pressure on the existing hospitals to be removed. Furthermore, the results indicated that the allocation-to-demand ratio can remain at an ideal level when disruptions occur by considering temporary facilities. Our analyses focus on: (1) Examining demand forecasting error and generated scenarios in the first phase, (2) exploring the impact of demand parameters on the allocation-to-demand ratio, total time and total risk, (3) investigating the strategy of utilizing temporary hospitals to address sudden changes in demand, (4) evaluating the effect of disruption to facilities on the supply chain network.