System for managing virtual private network and method thereof

Disclosed are a system for managing virtual private networks (VPNs) includes: terminals configured to transmit user data; a manager configured to transmit information for concealing networks and managing the VPNs; border gateways configured to decrypt the user data and perform a network address translation (NAT) procedure and a filtering procedure on the decrypted user data based on the information; and servers configured to receive the user data subjected to the NAT procedure and the filtering procedure, wherein the filtering procedure is a procedure discarding the user data to be transferred to the servers that are not allowed so as to allow the terminals to access only the allowed servers, the NAT procedure is a procedure changing an Internet protocol (IP) address used in a first network to an IP address used in a second network, and the first network and the second network are different networks.