Diaphragmatic bronchogenic cysts are rare, and very few cases have been reported in the literature to date. Herein, we present a 42-year-old male patient who had a diaphragmatic bronchogenic cyst with the radiologic appearance of an intrapulmonary lesion as the 32nd case in the English literature. We performed a videothoracoscopic excision of the cyst, which was later found to be originated from the diaphragm. Pathologic examination confirmed the diagnosis of the bronchogenic cyst. Diaphragmatic bronchogenic cysts may present as intrapulmonary lesions radiologically. Videothoracoscopic excision is a feasible treatment method for these lesions.