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Gender gaps in science, technology, engineering, and mathematics (STEM) occur as early as adolescence. In this paper, we explore the gender gaps in STEM through the lens of social identity threat, specifically looking at how eighth-grade students in science classrooms perceive and experience social identity threat. Using three years of the Trends in International Mathematics and Science Study (TIMSS) data (2011, 2015, 2019; n = 29,396), we examine the impact of perceiving and experiencing social identity threat, as well as the proportion of female science teachers in the schools, on students’ science achievement performance. Our results replicate the ongoing achievement gap in STEM among female adolescents, however, results indicate a greater impact for male adolescents compared to females.