Primary ciliary dyskinesia (PCD) is a genetic disease associated with abnormalities in ciliary structure and function. Although recurrent respiratory infection associated with ciliary dysfunction is a common clinical feature, there is no standardized treatment or management of respiratory infection in PCD patients. Here, we report that respiratory infection with PCD and intralobar sequestration (ILS) were treated successfully with clarithromycin before the surgical resection of ILS. A 15-year-old non-smoking Japanese woman was admitted for productive cough and dyspnea on exertion. Chest CT scan on admission showed complex cystic LESIONS with air-fluid level in the right lower lobe, and diffuse nodular shadows in the whole lobe of the lung. On flexible bronchoscopy examination, sputum and bronchiolar fluid cultures revealed Staphylococcus aureus (S. aureus). An electron microscopic examination of the cilia showed inner dynein arm deficiency. Administration of clarithromycin improved the lower respiratory tract infection associated with S. aureus. CT angiography after clarithromycin treatment demonstrated an aberrant systemic artery arising from the celiac trunk and supplying the cystic mass lesions that were incorporated into the normal pulmonary parenchyma without their own pleural covering. Based on these results, the patient was diagnosed with PCD and ILS. Because of the clarithromycin treatment, resection of the ILS was performed safely without any complications. Although further observation of clarithromycin treatment is needed, we believe that clarithromycin may be considered one of the agents for treating PCD.