A well designed public transportation system can provide convenience to the public, increase the profit of the transportation company, and reduce the cost to the society as a whole. The depot is an important part in the study of transportation systems. The choice of the capacity of the depots is a strategic decision. It will constrain the possible tactical decisions (such as vehicle planning) for a long time, due to the life-span of the infrastructure. It is therefore important to study the impact of the options before they are implemented. The transportation company now is facing the problem that there is no appropriate tool in the decision support system to assess the capacity of the depots and the vehicle planning on the deadhead-kilometer (non-value added trips) and the robustess of the service. The simulation model is an appropriate method for the main part of the study. It can be used to evaluate the key performance indicators of deadhead-kilometer and average delay time, to study the complex interactions among the different elements, and to improve the understanding of the behaviors of the transportation system. The simulation model is useful for evaluating both strategic decisions and tactical decisions. The analyzing tool is designed following the methodology of systems engineering. First the requirements were gathered and translated into specification. The design was then conducted to fulfill the requirements on the conceptual level. Specification of the key classes were then concluded from their functionalities and relationships. The detail design came out with detailed attributions and methods of the classes. The analysis is based on a part of the network which consists of five service lines. According to the analysis, compared to the current design (Scheveningen, Zichtenburg and Lijsterbes), the future alternative with “Remise Zuid” depot and closing down “Lijsterbes” depot achieves 18% reduction on average delay time, but with a cost of 15% of increase in deadhead-kilometer. With the ratings obtained from the policy advisors of HTM, the alternative with “Remise Zuid” outperforms the design of current situation on the overall performance. Though the methodology applies to the entire network, the analysis results so far portaits the impact on these five lines. A more comprehensive study can be conducted with the same method and the input data covering all the operating lines. Some improvement can be made on the management of depots by a better the training of the employees and a clearer definition of job responsibilities.