The performance appraisal system is considered an important factor for managing human resources in higher education institutions (HEIs). More importantly, when Information System (IS) is utilized for assisting such efforts, it inevitably makes the HEIs more efficient and competitive. This research attempts to integrate performance appraisal using competence-based appraisal (CBA). From this system, the HEIs are supposed to able to manage all activities related to their human resources and carriers. The methodology implemented in this research is by making the software of CBA model (the concept) and then the try out was done to find out both the weaknesses and strengths of the software, and finally the improvement was conducted as well. In addition, the evaluation of these software covers the aspects of validity and reliability testing so that the software are really proved to be completely applicable. The results provide the HEIs with information about both the weaknesses and strengths and therefore the system was made perfect based on such findings. It can be concluded that using CBA in HEIs, all the activities related to human recourses in HEIs can be rated. Thus, this CBA system enables the HEIs to do their human resources appraisal more accurately.