Anxiety is the most common mental health problem that occurs with Autism Spectrum Disorder (ASD), and due to creating a more inclusive learning environment, children with ASD are placed in general education classrooms. Thus, addressing anxiety problems for children with ASD in school settings become critically important. This systematic review and meta-analysis investigated the current qualities of studies and the effects of school-based interventions for reducing anxiety in children with ASD. The study included six studies with a total of 165 participants. A random-effect meta-analysis yielded a moderate overall effect (g = − 0.58, 95% CI [− 0.96, − 0.20], z = − 3.01, p < .05) with no significant heterogeneity, Q (5) = 7.31, p = 0.20. Findings of the systematic review indicated that school-based interventions for anxiety problems are still in the early stages, and studies showed significant issues with adaptations of current clinical-based interventions and anxiety measurements to use in school settings for children with ASD. Interpretation of these findings and implications are discussed.