Background Learners in the correct understanding of physics concepts express their inability, so change in the way of teaching the concepts of physics is necessary; in fact that effective training is learning materials actively involved in the construction of the mind. The aim of the present study is to study the effect of computer simulation based on constructivist approach to remove the misconception in physics course. Methods The research procedure is quasi-experimental with pretest- posttest and control group design. The population consists of all male and female secondary school students in Yazd (2009). This research includes 216 students in 2nd grade of high school in Yazd province. The sample is randomly assigned to experimental and control groups. The data collection tool is a questionnaire, using a panel of experts to verify the validity and using Cronbach’s alpha as75% to verify the reliability. For statistical analysis, software SPSS version 16 is used to examine the questions of the t-tests. Results The results of the analysis of data using statistical t independent groups showed that. There are significant differences in the effectiveness of computer simulation based on constructivist approach which remove the misconception in physics course (df = 160.53, t = -10.45, sig = 0.00, P < 0.01). Conclusions Based on the results of the present study, ways of presenting concepts with the help of computer simulation based on constructivist approach is an effective component to remove the misconception in physics course.