Six-Sigma has been the most influential management innovation program since Motorola first invented in 1987 and its application has extended to non-manufacturing processes such as transactional process and R&D process. Some container terminals in Korea, they try to introduce and implement Six-Sigma projects to improve the efficiency of terminal operation. There are some differences in Six-Sigma implementation between manufacturing process and non-manufacturing process. In this paper, we propose an implementation procedure and framework for Six-Sigma project, which are suitable for container terminal in harbor. This paper also presents priority in Six-Sigma topics for container terminal, that is confirmed from a BB(black-belt) workshop outcome. We testified the efficiency of the proposed implementation procedure through an empirical case study for Six-Sigma projects in a container terminal.