A vulnerability assessment is essential for the efficient operation of a physical protection system (PPS). Previous assessment codes have used a simple model called an adversary sequence diagram. In this study, the use of a two-dimensional (2D) map of a facility as a model for a PPS is suggested as an alternative approach. The analysis of a 2D model, however, consumes a lot of time. Accordingly, a generalized heuristic algorithm has been applied to address this issue. The proposed assessment method was implemented to a computer code; Systematic Analysis of physical Protection Effectiveness (SAPE). This code was applied to a variety of facilities and evaluated for feasibility by applying it to various facilities. To help upgrade a PPS, a sensitivity analysis of all protection elements along a chosen path is proposed. SAPE will help to accurately and intuitively assess a PPS.