IoT technology is growing very fast and one of the requirements of this technology is integrating different communications protocols and networks. In an IoT network, security of such a heterogeneous and large network is very important. Transport systems are part of this super network and in-vehicle protocols are used in such systems. Unfortunately, the Controller Area Network (CAN) protocol, the most popular protocol in the systems, designed without security in mind. In this paper, the Advanced Encryption Standard (AES), an encryption algorithm, is used to prevent masquerade and replay attacks in order to secure CAN protocol to an appropriate level. The paper has a plan to explore for an efficient implementation of AES encryption algorithm for the communication protocol. These implementations have been evaluated on an FPGA ML605 development board. The best implementation of the AES among 8-, 16-, 32- and 64-bit data paths has been investigated. The most important criteria for the protocol in these AES designs are such as consumed power, area, and cost in addition to providing better throughput. The 64-bit structure of the designed AES is selected which has the frequency of 21.4 MHz, significant throughput of 412.39 Mbps, reasonable area of 784 slice on Spartan III FPGA.