Origin verification is regarded most essential for FTA performance administration. This administration is divided into direct and indirect system where Korea has adapted indirect system to Korea-EU FTA while direct system to Korea-USA FTA. A comparative analysis was conducted on the system of origin verification and provisions contained in preferential tariff law of each countries. The study finds that Korean origin verification system is a bit lack of procedural provision resulting in less protection of domestic trader's rights. Another point is that Korean Customs Authority is weak, in respect of organization and man power, to protect illegal bilateral tariff application by counter part FTA countries. And therefore this study suggests the policy makers to arrange detailed FTA origin verification procedures with earliest meeting with counter part FTA countries, and further stress that make up of organization and man power for origin verification in a timely manner.