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The present study, which was conducted in Timss 2007 framework, aims to examine the effectiveness of teaching critical thinking on students’ academic achievement in mathematics and science. Research design was Semi-experimental. Research sample (With available sampling method) included two classes of third grade students in Eghbal middle school in Baharestan, Tehran, Iran in 2014-15 which were randomly assigned to experimental and control groups. Afterwards, the experimental group received critical thinking teaching for 12 sessions, while the control group received no training during this period. The data were gathered using parallel forms of Timss 2007 study, which were implemented in three periods. The data were analyzed through Analysis of Covariance (ANCOVA), and t-test. Results showed that critical thinking teaching could considerably improve students’ performance in mathematics and science in domains of reasoning and applying; however, no significant relationship was revealed between critical thinking teaching and students’ performance in the domain of knowing. Findings of the follow up test, in addition, indicated a significant decrease in applicants’ scores of experimental group. It can be concluded that critical thinking teaching should be brought into sharper focus in syllabuses of middle schools as its principles could not only resolve students’ problems in academic issues but they also would result in improving performance of students in the domains of mathematics and science.