Intelligent Tutoring System (ITS) is an interactive e-learning tool to help students learn independently. Currently, the implementation ITS is still in laboratory scale, means ITS has not been used in large scale using internet technology. One of the difficulties is ITS has not fulfill yet the learning needs. The main requirement of current learning based-competency is the high number of students in mastery learning, on the other hand current learning activities could not overcome the problems of student characteristics and different learning speed in each student as well. The concept of mastery learning is an approach used in competency-based learning, which consists of repetition of learning for slow students, mastering for good progress students, and enrichment for fast students. In this paper, the model of ITS is designed to accommodate the competency-based mastery learning needs and be able to follow learning speed of each student. The design of ITS has learning sequences and gradually test student`s cognitive level. It could measure the position of student`s cognitive knowledge, be able to guide to reach mastery level, and give challenges for smart students.