The aim of this study is to address the decline of self-esteem in puberty from a viewpoint of development of thinking, especially critical thinking disposition. The sample consists of 633 junior high school students from four schools. We conducted nine separate questionnaires. We first estimated the mean pattern of self-esteem. It showed that self-esteem declines until Time 5 (Grade 7) after that it increased; however, there was more variation after Time 5. Then we examined self-esteem across five different time points to address the decline by using a latent growth curve model. The model showed an acceptable fit to the data. The change of Individual differences of self-esteem were shown to be related to critical thinking disposition (Time 1). The results revealed that the development of critical thinking in puberty had a negative effect on the change of self-esteem: if students have a higher level of development critical thinking disposition, it predicts that their self-esteem will decline. Thus, it appears that the development of thinking would be related to the decline of self-esteem in puberty.