The most important protective measure in the pandemic process is a vaccine. The logistics and administration of the vaccine are as important as its production. The increasing diffusion of electronic devices containing geo-referenced information generates a large production of spatial data that are essential for risk management and impact mitigation, especially in the case of disasters and pandemics. Given that vaccines will be administered to the majority of people, it is inevitable to establish vaccination centres outside hospitals. Site selection of vaccination centres is a major challenge for the health sector in metropolitan cities due to the dense population and high number of daily cases. A poor site selection process can cause many problems for the health sector, workforce, health workers, and patients. To overcome this, a three-step solution approach is proposed: (i) determining eight criteria using from the experience of the advisory committee, (ii) calculating criterion weights using Analytic Hierarchy Process (AHP), and performing spatial analysis of criteria using Geographic Information System (GIS), (iii) assigning potential vaccination centres by obtaining a suitability map and determining service areas. A case study is performed for Bağcılar, Istanbul district, using the proposed methodology. The results show that the suitable areas are grouped in three different areas of the district. The proposed methodology provides an opportunity to execute a scientific and strategic vaccination programme and to create a map of suitable vaccination centres for the countries.