The present invention relates to a system and method for operating an end-to-end security channel between an IC card and a server on a communication network. A method for connecting an end-to-end security channel between an IC card and a server on a communication network includes the steps of: generating, by the server, a random number Rs for transmission to the IC card, generating an E(Rs) by encrypting the random number Rs by a user public key, and transmitting the E(Rs) to the IC card through the communication network; receiving, by the IC card, the E(Rs) through the communication network and extracting the random number Rs by decrypting the E(Rs) by a user private key; generating, by the IC card, a random number Rc to be transmitted to the server, generating a session key K′ by the random number Rs and the random number Rc, and generating a first card verifier MAC by encrypting the random number Rs by the session key K′; transmitting, by the IC card, the random number Rc and the first card verifier MAC to the server through the communication network; receiving, by the server, the random number Rc and the first card verifier MAC through the communication network, generating a session key K by the random number Rs and the random number Rc, and generating a first server verifier MAC by encrypting the random number Rs by the session key K; and comparing, by the server, the first card verifier MAC and the first server verifier MAC to certify the session key K.