The purpose of this study is to examine the relationship between student self-concept and achievement in science in Taiwan based on the big-fish-little-pond effect (BFLPE) model using the Trends in International Mathematics and Science Study (TIMSS) 2003 and 2007 databases. Hierarchical linear modeling was used to examine the effects of the student-level and school-level science achievement on student self-concept of learning science. The results indicated that student science achievement was positively associated with individual self-concept of learning science in both TIMSS 2003 and 2007. On the contrary, while school-average science achievement was negatively related to student self-concept in TIMSS 2003, it had no statistically significant relationship with student self-concept in TIMSS 2007. The findings of this study shed light on possible explanations for the existence of BFLPE and also lead to an international discussion on the generalization of BFLPE.