Many interventions have been implemented to increase STEM aspirations among high school students. However, recent research has pointed out the possibility that the self-perception of the humanities and sciences is formed at a stage prior to high school. In this study, we hypothesized that a strong self-perception of the humanities and sciences is already formed at the junior high school stage, and examined the validity of this hypothesis through a secondary analysis of a nationwide survey. Specifically, using publicly available data from the Parent and Child Survey on Children’s Life and Learning, an ongoing longitudinal survey since 2015, we examined the timing of awareness of one’s aptitude for the humanities and sciences (Analysis 1), the evolution of self-perception of the humanities and sciences (Analysis 2), and the predictability of future choice of humanities or sciences (Analysis 3). The results showed that self-perceptions of the humanities and sciences were fixed from the third year of junior high school to the third year of high school, and that machine learning using data from the third year of junior high school could predict the future choice of humanities or sciences with a certain degree of accuracy (approximately 70%).