There is evidence that student beliefs about science and classroom instructional strategies are related to achievement outcomes. This study was designed to examine relationships between student beliefs about science, instructional activities, and science achievement of elementary-school students in Japan. Students included in this analysis were 4,006 students from the TIMSS 2003 Population 1 (9-year-olds) International Sample from Japan. Variance estimation techniques for complex sampling designs were employed in this study. Cooperative learning activities and active learning strategies were positively associated with science achievement. In addition, these findings indicated that student beliefs about science were significantly related to achievement, even after considering the effects of teaching activities. Students who held positive beliefs about their science ability earned higher test scores while students who expressed negative comparisons of themselves to other students showed lower science test scores. These results indicate that science beliefs and instructional activities should be examined simultaneously when assessing factors related to science achievement. (Contains 1 table.)