Using original survey data from parents of children in kindergarten through junior high school in Tokyo, Japan, we find that parents exhibit stronger preferences for sons over daughters to participate in extracurricular STEM activities, with the gender gap widening as children age. Parents aspiring for their children to pursue STEM degrees prioritize science classes more, a preference more often directed toward boys. These gendered differences affect children’s early exposure to science. Since Japanese students choose between science and humanities tracks by eleventh grade, early disparities may limit girls’ opportunities. Promoting equal STEM access is crucial to reducing these gender gaps.