OBJECTIVES: As the only health technology evaluation institution in Korea, National Evidence-based Healthcare Collaborating Agency has made efforts to establish the topic selection model of comparative effectiveness research which corresponds to Korean situations in order to revitalize it since 2012. METHODS:  As a result of preparing thetopic selection process of the comparative effectiveness research according to these efforts and of conducting model operations in 2012, solution to access to the proposal process of research topics and a close examination of research methodologies was proposed as improvement point. RESULTS: Accordingly, web-based research topic proposal systems(www.necacer.re.kr) were designed in order to solve access to the proposal process of research topics and to increase transparency of the early stage of research in 2013. To make a close examination of the possibility of research performance in multidisciplinary fashion, evaluation systems of three stages were divided to operate but web-based design which is the same as topic proposal systems was done reflecting the evaluator's geographical access etc. Concretely, web-systems for topic proposal are composed of writing proposed research topic, writing proposed content of a topic, and confirming and submitting stages after writing basic information after login, and evaluative web systems were composed as follows: Step 1 is composed of quantitative evaluation based on 6 standards, step 2 qualitative evaluation based on 6 standards, and step 3 investigation process based on 4 standards in relation to research topics refined. CONCLUSIONS: It is conceived that Korean web-based topic selection systems of comparative effectiveness research prepared systematically taking Korean situation into consideration will be able to contribute to improving qualitative aspects of research and enhancing researchers' credibility by transparent opening the whole process of proposing, selecting and confirming topics.