Under the current Model Core Curriculum for Pharmaceutical Education, competencies and program-level learning outcomes are not differentiated; furthermore, how competencies are developed by specific behavioral objectives, which are subdivided by specialty, needs to be clarified. A clear vision for ensuring academic as well as clinical competencies in Japanese pharmaceutical education, which emphasizes research and education in basic fields, is needed. Standardization is necessary to ensure improvement in quality over time. Thus, it is necessary to establish a model core curriculum as a standard. First, we assigned students a task designed for them to pursue outcome-based education from the perspective of developing competencies. Second, students learned about the importance of “conceptual understanding”, which enables them to form generalizations and principles that enable them to deal with new situations. Finally, we discussed the specifics of how to transfer understanding in the cognitive domain and proposed a “concept-based curriculum” that considers a hierarchy of competencies that includes the non-cognitive domain. In addition, we created a draft of a form that had check items for incorporating it into a real curriculum with an eye to practical use. The method used in the present study of organizing a curriculum corresponding to qualitatively different cognitive, metacognitive, and action systems may be applicable to other professions in the medical field.