Vehicle systems are controlled by embedded electronic devices called electronic control units (ECUs). These ECUs are connected together with network protocols. The Controller Area Network (CAN) protocol is widely implemented due to its high fault tolerance. However, the CAN is a serial broadcast bus, and it has no protection against security threats. In this paper, we propose a fast stream cipher based on a chaos neural network (CNN) that is able to generate pseudo-random numbers at a high speed, faster than that of the Advanced Encryption Standard, to protect ECUs on the CAN bus by encrypting CAN messages. We discuss the chaotic orbit of the CNN and statistical properties of pseudo-random numbers from the CNN. For a stream cipher, it is very important to share the symmetric key. We designed a symmetric key that is shared with ID-based encryption without the need to use digital certificates. We evaluated our method's performance with embedded boards and showed that the stream cipher is efficient for the embedded software of the ECU. Further, it does not need a hardware security module to accelerate the encryption.