This case report describes the orthodontic treatment of a 2-year-old female with Apert syndrome, initially admitted to the Clinic of Congenital Abnormalities in the University Dental Centre of Medical University of Silesia in Katowice in 2004. Following craniofacial surgery for premature skull fusion, the patient exhibited characteristic Apert syndrome features, including premature fusion of skull bones, midfacial hypoplasia, and syndactyly. Removable appliances were used between 2007 and 2013 to manage dental development and teeth loss, followed by craniofacial osteoplasty in 2013–2014 to correct significant maxillary underdevelopment. Fixed orthodontic treatment was initiated in December 2014, focusing on aligning teeth, correcting malocclusion, expanding the upper arch, and managing crowding. Despite treatment challenges, such as poor oral hygiene the 6-year orthodontic treatment yielded a satisfactory functional and aesthetic outcome. The patient achieved correct overjet and overbite, reduced crowding, and improved jaw relations, though some occlusal problems, including a residual posterior crossbite and minor crowding, persisted. Almost 4-year follow-up demonstrated stable results, although bruxism was developed, requiring a nightly splint. Continued follow-up is essential for managing long-term stability in this complex case.