This report describes the long-term follow-up of a 10-year-old female patient with Joubert syndrome with short stature and brachydactyly. She presented with hyperpnea alternated with hypopnea, uncontrolled jerking eye movements, and hypotonia during early infancy. She was diagnosed with Joubert syndrome based on clinical symptoms and typical MRI findings at 5 months of age. Abnormal ventilation and eye movements disappeared at around 4 years of age. Head circumference kept within normal range for her age, but her height and weight growth were markedly retarded. Simple X-ray showed an enlarged skull with increased digital markings, hypoplasia of facial bones, and abnormal enchondral bone formations in hands and feet. This article is the first report of Joubert syndrome with peripheral dysostosis.