A rare case is described of an intrathyroidal branchial cleft-like cyst in neonate. The patient was a newborn girl with a mass in the left lateral neck. The ultrasonography and computed tomography revealed a cystic lesion in the left thyroid. The lesion was enucleated surgically from the thyroid. Histologically, the cyst was lined by squamous or columnar epithelium and contained inflammatory cell infiltraion, thyroid and parathyroid tissue. The patient has been doing well without any evidence of thyroid dysfunction for 15 months.