Crouzon and Apert syndromes are rare syndromic craniosynostoses frequently associated with craniofacial and dental anomalies, including tooth agenesis. Although individual studies have reported tooth agenesis prevalence data in specific populations, no attempts have been made to systematically synthesise these data. This systematic review and meta-analysis evaluated the prevalence and patterns of permanent tooth agenesis in patients with Crouzon or Apert syndromes. The study followed a pre-registered protocol (PROSPERO CRD42024581856). Two independent investigators conducted a literature search in MEDLINE (via PubMed), Web of Science, Embase, ProQuest, and Google Scholar to identify studies on permanent tooth agenesis in individuals with Crouzon or Apert syndromes. Studies were deemed eligible if they reported on permanent tooth agenesis in patients diagnosed with Crouzon or Apert syndromes. Risk of bias was assessed using the Joanna Briggs Institute tool. Random-effects and inverse variance heterogeneity meta-analysis models were used for data synthesis. After database search, deduplication, and screening, seven studies were included, comprising a total of 89 individuals with Apert and 77 with Crouzon syndrome. The estimated overall prevalence of permanent tooth agenesis, excluding third molars, was 37% (95% CI: 28%-48%) in individuals with Apert and 31% (95% CI: 17%-46%) in those with Crouzon syndrome. In Apert syndrome, the most common tooth agenesis pattern was the bilateral absence of the mandibular second premolars, followed by the absence of the left maxillary lateral incisors and the bilateral absence of the maxillary lateral incisors. In Crouzon syndrome, the most frequent tooth agenesis pattern was the absence of the right mandibular second premolar, followed by the bilateral absence of the mandibular second premolars. Individuals with Crouzon or Apert syndrome present a high prevalence of tooth agenesis. Early diagnosis of missing permanent teeth is essential to optimise long-term treatment planning and improve functional and aesthetic outcomes. However, the evidence is limited by small sample sizes and heterogeneity across included studies.