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Despite the growing interest in pair programming in K-12 settings, its impact on cognitive and affective outcomes and the factors influencing these outcomes remain unclear. This meta-analysis evaluates the effects of pair programming on K-12 students’ cognitive and affective outcomes. For cognitive outcomes, we analyzed 10 primary studies with 18 independent samples, revealing a moderate effect size (g = 0.28, p = .013). For affective outcomes, the analysis included 7 primary studies with 8 independent samples, showing no significant effect (g = 0.13, p = .10). Moderator analyses (i.e., school levels, pair formation, and programming tasks) on cognitive and affective outcomes further offer insights into optimizing the effectiveness of pair programming in K-12 educational contexts.