It is reported by the Ministry of Education, Science, and Technology that professors of national universities are paid annually based on their performances in phases starting from the year 2011. The new professor salary system is expected to bring considerable changes to the evaluation of faculty works in national universities. The most important issue of the change is that the new professor salary system, contrary to the previous merit-based salary system of which the effect is limited only to the academic year, has cumulative effects on professors' salaries until the last year of their employment. So, many issues related to the evaluation of faculty works needs to be carefully examined and reviewed. That is why our study has been started. From the reason, the study has been focused on finding problems, searching and providing effective solutions of faculty performance evaluation issues such as categorization of academics for the evaluation purpose, setting-up of tracks and weights based on individual demand, equation of the performance scores, grouping by performance levels, deciding appropriate amount of payment, evaluation areas and criteria, evaluation period, qualitative evaluation, and so on.