Bronchogenic cysts are congenital malformations of the embryonic tracheobronchial tree and are the most common cause of mediastinal cysts, encountered mainly in pediatric patients and young adults. Conservative treatment has been proposed for asymptomatic patients. However, malignant transformation occurs occasionally and the clinicopathological features of secondary malignancy are not well characterized. In this report, we present a carcinoid tumor found in the thymic bronchogenic cyst of a 41-year-old female complaining of mild chest pain. The thymic tissue also shows follicular lymphoid hyperplasia. Atypical imaging features were found in her chest computed tomography. Additional 22 cases of bronchogenic cysts with malignant transformation were also reviewed from the literature. The clinicopathological data were summarized. The tumorigenesis of these tumors is unclear, but bronchogenic cysts of the lung may undergo malignant changes at a younger patient age and more frequently than mediastinal ones. Carcinoid tumors were also seemingly overrepresented in mediastinal cases. Some atypical imaging features may serve as clues for early detection and guide clinical management.