A flexible network security system and method is provided for permitting a trusted process. The system includes a port monitoring unit for extracting information about a server port being used through a network communication program, an internal permitted program storage for extracting information about a program for which communication is permitted by the firewall and registering the extracted information, an internal permitted port storage registering the extracted information if the network communication program is registered in the internal permitted program storage; and a device for making the firewall flexible, determining whether a destination port of a packet of inbound traffic has been registered in the internal permitted port storage, and if the destination port has not been registered, transmitting the corresponding packet to the firewall, and if the destination port has been registered, allowing the corresponding packet to bypass the firewall.