The prototyping is the efficient method from many methodologies of software engineering approaches. The traditional waterfall model is suitable for the well understanding requirement and large project. The pilot project of research tracking system had never been established before in University of the Thai Chamber of Commerce (UTCC). The staffs in the research departmentmanually manage the research tracking system of researchers funding by UTCC which are approximately 2030projects a year. The prototyping methodology was chosen to apply to this work. The paper describes how the prototyping was created according to the theory compare to the real case scenario situation. The pros and cons of prototyping techniques are addressed in the paper. The recommendations and the observations from the practices were also taken into the consideration in this work.