Past meta-analyses in mental health interventions failed to use stringent inclusion criteria and diverse moderators, therefore, there is a need to employ more rigorous methods to provide evidence-based and updated results on this topic. This study presents an updated meta-analysis of interventions targeting anxiety or depression using more stringent inclusion criteria (e.g., baseline equivalence, no significant differential attrition) and additional moderators (e.g., sample size and program duration) than previous reviews. This meta-analysis includes 29 studies of 32 programs and 22,420 students (52% female, 79% White). Among these studies, 22 include anxiety outcomes and 24 include depression outcomes. Overall, school-based mental health interventions in grades K-12 are effective at reducing depression and anxiety (ES = 0.24, p = 0.002). Moderator analysis shows that improved outcomes for studies with anxiety outcomes, cognitive behavioral therapy, interventions delivered by clinicians, and secondary school populations. Selection modeling reveals significant publication and outcome selection bias. This meta-analysis suggests school-based mental health programs should strive to adopt cognitive behavioral therapy and deliver through clinicians at the secondary school level where possible.