Abstract The existence of gender peer effects has been well-documented, yet regarding estimates that are best-suited for policy formation, the literature finds somewhat mixed results. This article builds on the gender peer effects literature in a number of ways. First, we focus on early elementary school students, for which fewer studies exist. We also test whether effects in early elementary grades are subject-specific. Contrary to findings for older grade levels, we find that estimates by gender are subject-specific for the early elementary grades. Second, previous studies using similar estimation have focused on very different geographical areas, while this study makes use of nationally representative elementary school data for the United States. Third, we explore whether effects vary across grades, for which the existing literature finds mixed results. We find that the negative subject-specific effects of having a higher proportion of boys in the classroom increases in magnitude across grades, with insignificant effects in kindergarten, negative and significant by first grade, and larger negative and significant effects by third grade. Our findings suggest that a more balanced gender mix in the classroom is optimal for both reading and math comprehension for both boys and girls. However, regarding math performance, there is also suggestive evidence that a 100% separation of genders could improve girls’ math performance without consequences for boys’ math performance, motivating further research into single-gender subject-specific instruction.