In this paper, we suggest a practical and flexible system architecture for JTAG(Joint Test Action Group) protection of application processors. From the view point of security, the debugging function through JTAG port can be abused by malicious users, so the internal structures and important information of application processors, and the sensitive information of devices connected to an application processor can be leak. This paper suggests a system architecture that disables computing power of computers used to attack processors to reveal important information. For this, a user authentication method is used to improve security strength by checking the integrity of boot code that is stored at boot memory, on booting time. Moreover for user authorization, we share hard wired secret key cryptography modules designed for functional operation instead of hardwired public key cryptography modules designed for only JTAG protection; this methodology allows developers to design application processors in a cost and power effective way. Our experiment shows that the security strength can be improved up to $2^{160}{ imes}0.6$second when using 160-bit secure hash algorithm.