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One challenge of US science education is the achievement gap between male and female students. Using PISA 2015 US data and latent moderated structural equations, this study examined whether engaging students in science practices and teacher’s scaffolding discussion activity favor male students’ science learning and how teachers’ scaffolding discussion activity moderates the relationship between students’ science practices and science achievement across gender. The results showed that student independent science practices either negatively or not significantly predict science achievement. Significant interactions were found between teacher’s scaffolding discussion activity and student science practices. The negative relationship between students’ science practices and their science achievement was significantly reduced by high teacher scaffolding activity across gender.