Mega-events are held in a city, or more, during a limited time, which requires special attention to the infrastructure and the offered services. The Hajj event, hosted in Makkah -Saudi Arabia, is considered as an excellent example of religious mega-events. The field of computer modeling and simulation is one of the main technical tools that help in developing and understanding the risks of crowds and studying the safety means during organizing of many major events in the world. This paper focuses on using computer simulation to optimize the pilgrims' shuttle-bus transportation system in Holy Sites (Mashaaer), as a case study of optimizing shuttle-bus Systems in Mega-Events using computer modeling. The objective of paper is to develop a model of the shuttle-bus transport system to give insights of the advantages of the use as an alternative for transporting pilgrims as well as to provide decision makers with a tool that could be used to select the best parameters of the system for the most efficient operation. For this purpose, pilgrims' evacuation time, traffic congestion and average trip time, from Arafat to Muzdalifa, are identified as the performance measures for evaluating the proposed transport system. The conducted simulation can be used to assess the current systems, recommend changes to the systems, and offer indicators and readings to assist decision makers.