Mucoepidermoid carcinoma (MEC) of the lungs is a rare type of lung cancer, mainly arising from the submucosal salivary type mucous glands of the large bronchi. MEC is classified into low- and high-grade subtypes based on its cytological and histological features, and this classification correlates well with prognosis. We report the case of a 36-year-old man diagnosed after an initial episode of obstructive pneumonia. CT and bronchoscopy revealed an endobronchial mass in the right S3 bronchus and distal atelectasis. Although biopsy is important for deciding the treatment plan, both pre- and intraoperative biopsy resulted in false negativity in this patient. The tumor was completely resected via right upper lobectomy, and the final pathological diagnosis was low-grade MEC. No evidence of disease was found 2 years after the operation without any adjuvant therapy. At (11; 19) translocation with the associated CRTC1-MAML2 fusion oncogene is often recognized in cases of both salivary and pulmonary MEC. It is speculated that MEC is sensitive to EGFR-TKI therapy, which disrupts CRTC1-MAML2-induced proliferation signals via upregulation of the EGFR ligand amphiregulin.