This study investigated (1) whether self-esteem levels predict academic performance and (2) whether this relationship differs by gender. A total of 158 seventh-grade students (81 boys, 77 girls) at a Japanese junior high school were assessed for self-esteem using both a group-administered Implicit Association Test (IAT) and a self-report questionnaire. Students were classified into groups based on implicit and explicit self-esteem levels, and their academic achievement (standardized Z-scores) was tracked across five testing periods during the school year. While girls outperformed boys overall, students with higher explicit self-esteem—regardless of gender—achieved better academic results. However, patterns differed for implicit self-esteem: boys with high implicit self-esteem improved over time, whereas girls with similarly high levels experienced a decline. These findings suggest that excessive implicit self-esteem may hinder academic progress in girls.