Whole-school Social-Emotional Learning (SEL) programs demonstrate promise as an avenue for universally and equitably fostering student social and emotional wellbeing. This study used population data collected in 2015 to examine the association of Australian elementary (primary) school-based SEL programs with students' late middle childhood functioning (aged 11–12 years) on the five social-emotional competencies defined by the Collaborative for Academic, Social, and Emotional Learning (Self-Awareness, Self-Management, Social Awareness, Relationship Skills, and Responsible Decision-Making). A total of 18,643 Year 6 students self-reported competencies on the Middle Childhood Survey–Social-Emotional Learning, and 569 school leaders reported on delivery of SEL to these students via the Survey of School Promotion of Emotional and Social Health. Multi-level regression, accounting for school clustering, compared competency levels among students who did and did not receive SEL at school. Secondary analyses determined the strength of effects for students receiving programs with a high-quality evidence base, for programs supported by little or no empirical evidence, and for evidence-based SEL programs that provided a high degree of explicit teaching (i.e., structured teaching and skills practice) of the targeted social-emotional competencies, each relative to students receiving no SEL programs. Positive significant effects of SEL were observed on four of five competencies (excluding Responsible Decision-Making), with effects being strongest for empirically-evidenced SEL programs that provided explicit teaching of the targeted competency. No significant effects of under-evidenced programs were observed. This novel, population-level evaluation demonstrates the universal benefit of evidence-based SEL programs in supporting elementary school students' development of social-emotional competencies.