A rare case is described of intrathyroidal branchial cleft-like cyst associated with unusual heterotopic tissues including the salivary gland type tissue, fat, and cartilage. This coexistence in the thyroid gland has not been described previously, to our knowledge. The patient was a 7-year-old girl with a growing mass in the left lateral neck. The ultrasonography revealed a cystic lesion in the left thyroid. Histologically, the cyst was lined by squamous or respiratory-type epithelium resting on the fibrous tissue containing lymphoid tissues with follicle formation and solid cell nests (SCNs). This cyst was intimately associated with heterotopic tissues including lobules of well-differentiated seromucinous salivary glands, mature fat tissue, and islands of the cartilage. This association of branchial cleft-like cyst with SCNs and unusual heterotopic tissues in the normal thyroid suggests a possible origin from the SCN as ultimobranchial vestigial structures.