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It has become an important and challenging issue to foster students' concepts and skills of computer programming. Scholars believe that programming training could promote students' higher order thinking performance; however, many school teachers have reported the difficulty of teaching programming courses. Although several previous studies have attempted to develop friendly user interfaces to ease students' loads, teaching programming courses remains a big challenge for most school teachers. In this study, an online peer assessment-based system was developed to cope with this problem. The students could use the peer-assessment function to provide comments to peers, and review the feedback and scores from peers during the learning activity. A quasi experiment was conducted on four classes of 166 ninth graders of a junior high school located in southern Taiwan to examine the impacts of the developed system. Two classes of students were assigned to the experimental group, learning with an online peer assessment-based teaching strategy, while the other two classes were the control group, learning with the conventional teaching strategy. The experimental results showed that the students in the experimental group had better programming knowledge and skills as well as more positive learning attitudes and critical thinking awareness than those in the control group, revealing the benefits of the proposed approach.