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This study aimed at detecting the alternative conceptions that the tenth-grade students have regarding the topic “Atomic Structure” and the effectiveness of a Meta-Cognitive Strategy on changing their alternative concepts. The subjects of the study consisted of tenth-grade students at the Basic Cycle, intentionally chosen from two schools located in Al-Nuzha neighborhood in North Amman District, Jordan, affiliated to the UNRWA, one for boys and the other for girls. Two classes from each school were chosen and distributed randomly into experimental and control groups. The meta-cognitive instructional strategy was applied to the experimental group, where the conventional teaching strategy was applied to the control group. In order to determine students’ alternative conceptions, a test instrument was developed by the researchers to reveal these concepts. The validity of the test was established by asking a group experts and specialized educators to evaluate it, and their comments were taken into consideration. The results revealed that the students have many alternative conceptions related to atomic structure. It also revealed that there is a significant difference (α =0.05) between the experimental and control groups in the number of correct conceptions at the end of the study in favor of the experimental group, which indicates the effectiveness of the meta-cognitive instructional strategy in changing students' alternative concepts. On the other hand, there were no significant differences that can be attributed to gender or the interaction between methodology and gender. According to the results of the study, the researchers recommended organizing the content of science textbooks in accordance with the meta-cognition strategies, and training teachers to apply the meta-cognitive strategy in teaching science.