A 47-year-old man presented at our hospital with dry cough and an abnormal shadow on his chest X-ray. He was diagnosed with pulmonary nocardiosis after the detection of Nocardia spp. in bronchial lavage fluid. The species was identified as Nocardia asiatica by 16S rRNA gene-sequencing analysis. His condition was successfully treated with sulfamethoxazole trimethoprim. Because he had a history of male sterility resulting from sperm dysmotility and repeated episodes of tympanitis and bronchopneumonia, he was thought to have primary ciliary dyskinesia (PCD). Therefore a bronchial mucosa sample obtained by biopsy was analyzed by electron microscopy, and a diagnosis of PCD was confirmed. The findings of this case indicate that an abnormal mucociliary transport system may lead to the development of pulmonary nocardiosis, also that PCD should be considered as an underlying condition in an immunocompetent patient with pulmonary nocardiosis, which may have better prognoses in immunocompetent patients than in immunocompromised patients.