Studies heretofore have shown inconsistent results on the link of ASD to malocclusion. Herein, we aimed to compare the prevalence of malocclusion among children and adolescents with ASD compared with non-ASD healthy counterparts through a systematic review. The electronic search focused on five databases, PubMed, Web of Science, EMBASE, LILACS, and OpenGrey until January 2022, and followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines (PROSPERO No. CRD42022298023). Observational and intervention studies that compared occlusion characteristics of ASD individuals under 18 years old with healthy controls were included. Pairwise random effects meta-analyses of odds ratio (OR) were performed. Methodological quality was assessed by using the Joanna Briggs Institute Critical Appraisal Checklist for cross-sectional studies. A total of thirteen studies were included for qualitative analysis, and seven for quantitative analysis. The results presented a great heterogeneity and moderate risk of bias; thus, it was not possible to state that there is a risk of malocclusion in individuals with ASD. Future studies should be carried out with strict criteria in the choice of samples, control group, and diagnosis of malocclusion in order to meet the necessary requirements for greater methodological quality.