Background The median solitary maxillary central incisor syndrome (SMMCI) is a rare malformative syndrome consisting of multiple defects, mainly found on the body midline. It can be correlated to the etiopathological and phenotypic pattern of panhypopituitarism. This case-report describes the rare case of a patient suffering from SMMCI and panhypopituitarism, showing an unusual craniofacial morphology. Case presentation From the cephalometric analysis, a skeletal class III was identified (despite the other cases described in literature described as skeletal class II), derived from hypomaxillia and mandibular protrusion. A convex lip profile, with tendency to mandibular hyper-divergency, airway patency, anterior and posterior cross-bite were observed. At the clinical examination, a maxillary cant was evident on the frontal plane that appeared asymmetric, with the prevalence of the third lower part of the face. There were some dysmorphic signs such as: small nose, rectilinear eyelid line and reduced interocular distance. Conclusions The present clinical case shows how, despite the literature, SMMCI can be associated with a III skeletal class, with maxillary hypoplasia and mandibular protrusion. The interdisciplinary collaboration between dentist and pediatrician is therefore important for the early interception of the malocclusions associated with these syndromes.