A 68-year-old female consulted our hospital, complaining of a large mass on the left side of the neck. Computed tomography and magnetic resonance imaging revealed the characteristic internal architecture of the mass, in which a small cyst was located within a cystic mass, showing a "cyst-within-cyst" appearance. A final diagnosis of second branchial cleft cyst was made pathologically. A "cyst-within-cyst" appearance is not usually seen in a second branchial cleft cyst. This appearance may be attributed to several fine-needle aspiration biopsies for diagnostic purposes.