The Rasmussen Syndrome (RS) is a rare neurological disease, usually diagnosed in the 1st decade of life, leading to damage of the central nervous system. It is characterised by sudden seizures in previously healthy children. In this paper we present a case of a 14-year-old female patient with malocclusion who reported to the orthodontic clinic to start orthodontic treatment. The first symptoms of nervous system disorders manifested when the patient was 8 years old. Until then, the patient had been developing correctly. The interview revealed that at the age of 9 the patient was diagnosed with Lyme disease and a long-term antibiotics therapy was started. At the age of 10, the Rasmussen syndrome was diagnosed (the antibiotics therapy was discontinued) and confirmed by magnetic resonance imaging (MRI) and histopathological examination after brain biopsy. The study focuses in particular on the changes in the craniofacial skeleton and oral cavity, taking into account dynamically developing and increasing occlusion defects. The ethical aspect of the treatment has also been considered.