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This study aims to explore school effects on the gender gap in science achievement among Chinese eighth-grade students. There are three interrelated research questions: Is there a gender gap in science achievement? If yes, does the gender gap change over the years? And what characteristics of schools moderate the gender gap? We adopted three-level growth models to analyze 5-year longitudinal data. Results revealed that there was a significant gender gap in favor of boys, which was growing to be narrower over five years. school autonomy was the only salient moderator. Its positive effect was associated with smaller gender gap in the beginning, whereas its negative effect was associated with a slower rate of change of gender gap over the years.