Branchial cleft cysts, sinuses, and fistulas are the most common congenital lateral neck lesions in children. They arise as a result of an abnormal development of the branchial arches and their corresponding ectoderm-lined branchial clefts. Of these diverse anomalies, second branchial cleft lesions are the most common, accounting for approximately 95% of all branchial arch pathologies. We describe what is to the best of our knowledge the first reported case of an ectopic tooth in a branchial cleft anomaly. The patient was a young girl who had other congenital abnormalities and syndromic features and who was eventually diagnosed with Townes-Brocks syndrome. We describe the clinical presentation, management, pathologic analysis, and postoperative outcomes of this case, and we present a brief review of Townes-Brocks syndrome.