This paper discusses laboratory activities that can improve the meaningfulness of natural product chemistry course. These laboratory activities can be useful for students from many different disciplines including chemistry, pharmacy, and medicine. Students at the third-year undergraduate level of chemistry education undertake the project to isolate secondary metabolites from medicinal plants. This project provides opportunities for students to design their own activities to isolate secondary metabolites from medicinal plants. Students were exposed to skills as extraction, fractionation, purification, and structural elucidation of secondary metabolites. In this project, two secondary metabolites were successfully isolated from medicinal plants. The implementation of this project improved students' understanding of natural product chemistry.