Due to increasing demand of electrical energy and freshwater in Egypt, it is safe to assume that the decision makers will turn to nuclear power as the feasible alternative for energy. However, as time goes by, fewer sites will be available and suitable for nuclear power plant development. Site selection is a key phase of the siting process of a nuclear plant and may significantly affect the safety and cost of the facility during its entire life cycle. The siting of nuclear power plants is one of multi-criteria problems, which makes it complex. Many interrelated factors affect the process. Six constraints and twenty-two factors corresponding to safety, environment and socio-economy were considered in the siting study presented in this paper. Multi-Criteria Decision Analysis was applied during the selection of nuclear power plants site using GIS software. Three spatial decision making models were applied in this paper during site selection stage. The binary overlay (Boolean logic) with Low Risk approach in which the logical OR operator is used to determine the candidate areas. All constraints were represented in binary maps, combined and a masking layer was created to eliminate the lands considered as constraints in Arc GIS Software. The 22 factors were represented in normalized maps after unifying all of them to 0–1 score scales based on the philosophy of suitability criteria (factors) using the Weighted Linear Combination (WLC) method. The relative scores and weight of factors which were used in the maps conducted by pairwise comparison were fed into Expert choice software that runs the Analytic Hierarchy Process. Final composite map of potential site priorities were represented by several polygons produced in MCDA add-in as an open source tool in Arc GIS 10.1. Four sites, all located along the North western and the Red Sea coasts were chosen as Candidate sites after eliminating the lowest scoring sites The Analytic Hierarchy Process (AHP) was used to select a suitable site by pairwise comparison and by calculating eigenvectors using Expert Choice software. The sites were ranked to determine the most desirable site. The El Dabaa site was found to be most suitable, followed by the East El Negila site on the Mediterranean Sea.