Introduction: Apert syndrome is one of the rare forms of acrocephalosyndactyly, also characterized as the branchial arch syndrome, thereby affecting derivatives of the first and the second branchial arch. It represents autosomal dominant inheritance. It constitutes craniosynostosis, syndactyly of extremities, and dysmorphic facial features with significant oral manifestations. Case presentation: The presented case report emphasizes a 13-year-old female with a chief complaint of pain in left mandibular posterior tooth region. The patient was diagnosed with Apert syndrome at birth and presented with typical features such as craniosynostosis, syndactyly and dysmorphic facial features. The patient was active and playful and showed positive behavior towards dental treatment. Discussion: As the case represents rarity and similarity in features with other craniosynostosis syndromes such as Crouzon syndrome and Pfeiffer syndrome, it becomes a diagnostic dilemma. Thus, genetic counselling and early intervention form an essential part of treatment. As cases reported in Indian literature are deficient and typical features in the oral cavity are accustomed, a dentist should be acquainted with diagnosis and form a part of the multidisciplinary management team.