Background: The adenoid cystic carcinoma (ACC) barely arises in sites other than the salivary glands. Its presentation in the hypopharynx previously diagnosed as squamous cell carcinoma (SCC) is entirely unexpected. Case Presentation: A man was presented with a hypopharyngeal mass revealed by electronic laryngoscopy. Multiple biopsies pathologically showed well to moderately differentiated SCC. Six months after definitive concurrent chemoradiation, his endoscopy showed a recurrent mass in the same region before and pathology of gastroscopic biopsy showed moderately differentiated SCC of esophagus. The mass was removed after radical dissection. Histologic examination showed sheets and cords of tumor cells with basophilic matrix in hypopharynx known as ACC and moderately differentiated esophageal SCC. Conclusion: The documentation of metachronous ACC arising in hypopharynx following previous SCC would further supports the concern about multicomponent tumors in hypopharynx which is crucial in clinical practice.