Abstract Background/objective Craniofacial discrepancies have been associated with congenital dental anomalies. The aim of this study was to determine if there is any scientific evidence in the literature regarding the association between dental agenesis and craniofacial morphology. Materials and methods A systematic review and meta-analysis following the PRISMA Statement were conducted and registered in PROSPERO database. A broad search was conducted on databases (PubMed, Virtual Health Library, Web of Science, and Scopus) and grey literature. Articles that were selected based on predetermined eligibility criteria were assessed for quality and risk of bias according to the guidelines described by Folkes and Fulton. Those articles with similarities were submitted to meta-analysis using the RevMan 5.3 program. The certainty of the evidence was tested using the GRADE (Grading of Recommendations, Assessment, Development and Evaluation). Results An electronic search of 975 articles resulted in 12 articles. These and four articles identified through manual search were eligible to be assessed for methodological quality and the risk of bias. Eleven articles presented moderate to high methodological quality. The included articles observed a reduced mandibular plane, a smaller maxilla and more differences with the increase in the severity of dental agenesis. Seven articles were included in the meta-analyses. Dental agenesis presented smaller SNA angle (P < 0.0001/CI −1.74 [−2.55, −0.92]) with moderate certainty of the evidence; and smaller ANB angle (P = 0.01/CI −0.80 [−1.44, −0.17]), with low certainty of the evidence. Conclusions This systematic review and meta-analysis demonstrated that dental agenesis may be associated with specific craniofacial morphology. Further studies are necessary due to the variation of the certainty of the evidence. Conflict of interest none declared. Registration PROSPERO (CRD42017055882).