This study examined the characteristics of the National Assessment of Educational Achievement (NAEA) in Science according to gender. It investigated gender achievement differences in the science section of the 2010 NAEA, the ratio of gender difference in achievement, the ratio of correct answers within each content domain and behavioral domain, and the items which showed high differences between males and females. The results indicate first, that, for 9th graders, females outperformed males in academic achievement in science. Second, with respect to the ratio of correct answers, males outperformed females in the advanced and below basic level groups, but females outperformed males in intermediate level groups. Third, females outperformed males in knowledge and inquiry in the behavior domains, and in chemistry and biology in the content domains. Fourth, an analysis of the items showing the largest gender gap indicated that males outperformed females in interpreting data, while females outperformed males in the items concerned with daily life and items related to the memorization of rules. This research on gender differences in science will allow teachers to complement the weaknesses of students when they study science, and support improved instructional methods in science.