Since 2004, based on the reform of School Education Law in 2002, all of the universities in Japan are obligated to receive an accreditation evaluation conducted by the evaluation agencies with the authorization of MEXT for improving the quality of teaching and research, and release evaluation results to the society. This paper aimed to: 1) explore the changes of Japanese university evaluation system before and after World War II, 2) discuss the mechanism and the problems of accreditation evaluation, and 3) compare two evaluation agencies, the Japan University Accreditation Association and the National Institution for Academic Degrees and University Evaluation.