Worldwide Interoperability for Microwave Access (WiMAX) is a Metropolitan Area Network (MAN) wireless technology that provides broadband Internet access to both fixed and mobile users. Due to limited radio propagation range of wireless mobile devices and variable and unpredictable characteristics of wireless communication medium, there are certainly some effects of the speed of mobiles, and the amount of reliability provided by the underlying Transport Layer on the network performance. In this study, simulation of WiMAX networks is performed using Network Simulator 2 (NS2) to investigate the effects of Maximum Velocity and Pause Time of Mobile Stations and a comparative performance analysis of two commonly used Transport Layer Protocols, namely, Transmission Control Protocol (TCP) and User Datagram Protocol (UDP), is also conducted. TCP variant New Reno is used. For more realistic simulation, NS2 scene generation script is modified. Experiments demonstrate that performance of a WiMAX network is relatively stable when TCP is used. TCP shows overall better performance, especially in case of Packet Delivery Ratio and Average End to End Delay, while throughputs are almost similar for both the protocols, which prefers the use of TCP over UDP in mobile WiMAX networks for all applications.