Despite the well-established link between children’s executive function and behavioral adjustment, it remains unclear whether the hot and cool aspects of executive function are uniquely associated with children’s behavioral problems. Using longitudinal data spanning in the grade school (N = 1,140), this study aimed to examine whether hot and cool executive function skills may be uniquely related to the development of behavioral problems. Hot and cool executive function skills were measured with tasks, standardized tests, and questionnaires at 54 months and in the first grade, respectively. Internalizing and externalizing problems were evaluated by teachers using questionnaires throughout the grade school. The results indicated that, independent of each other, hot and cool executive function skills were uniquely and negatively related to the development of internalizing and externalizing problems over time at the between-individual level, adjusting for within-individual fluctuations. Moreover, internalizing and externalizing problems were positively related at the between-individual level across the grade school. Findings provide needed evidence to clarify the relations between hot and cool executive function and children’s behavioral problems, emphasizing the importance of both aspects of executive function in understanding the development of behavioral problems in school-age children.