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Background: The purpose of the present study is to investigate the effect of classroom management based on cooperative learning approach on the educational achievement of students in elementary sixth in science course. Methods: The method of this study was quasi-experimental and with pre-test -post-test using two control groups and two experimental groups. The statistical population was elementary sixth students in Piranshahr primary schools in schooling year 2011 -2012. Sample size was 120, and through multi-stage cluster sampling, 60 students were classified into experimental groups and the other 60 students into control groups. Classroom management based on cooperative learning approach was used in the experimental groups while that based on traditional teaching approach (lecture) was used in the control groups. The study instruments were inclusive made-researcher educational achievement tests. All the tests were consistent in terms of validity and reliability coefficient (0.91). Data was analyzed by descriptive statistics (mean and standard deviation), and inferential statistics (T test). Results:The results revealed that the educational achievement of students having classroom management based on cooperative learning approach with mean scores (15.69) were more involved in learning than students who are based on the Traditional approach (lectures) with mean scores (14.10), were learning (P < 0.01). In the collaborative groups between the two groups, boys with the mean scores 15.63 and girls with the mean scores 15.75 were not significantly different (P < 0.01). Conclusions: Based on the present results, implementation of classroom management based on cooperative learning approach can have positive effects on educational achievement in Science class.