An 8‐year‐old male Yorkshire terrier was presented to the Tufts Veterinary Hospital for evaluation of increased respiratory effort. A mediastinal mass composed of a spindle‐cell thymoma within a bronchogenic cyst was diagnosed with computed tomography thoracic imaging, ultrasound‐guided fine‐needle aspirate biopsy, and histopathologic evaluation after surgical removal. Histologic evaluation showed a multilocular cyst structure as well as a mass characterized by spindle to polygonal thymic epithelial cells. The cyst was characterized by a lining of ciliated pseudostratified respiratory epithelium. To the authors' knowledge, this is the first report of a spindle‐cell thymoma being associated with a mediastinal bronchogenic cyst in a dog.