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Bilateral second branchial cleft fistulae are very rare and usually arise from the incomplete obliteration of the branchial apparatus during the embryonic period. Here, we present the clinical characteristics and surgical treatment of a case with bilateral second branchial cleft fistulae coexisting with bilateral pre-auricular fistulae. A 32-year-old man with complaints of a mucus-like discharge that was occasionally secreted on both sides of his neck at 2 years of age when swallowing or pressing the upper area of the two openings. He underwent surgical treatment. The fistulae tracts were traced ascending to the area adjacent to the internal and external carotid arteries, passing the glossopharyngeal and hypoglossal nerves, and opening into the tonsillar fossa finally. The correct diagnosis and definitive surgical excision should be made by a doctor who is familiar with the history, clinical examination, and anatomic structure of the different types of branchial anomalies.