We report an extremely rare case of branchial cleft-like cysts in Hashimoto's thyroiditis. The patient was a 77-year-old man with a growing mass in the anterior neck. Ultrasonography and computed tomography revealed a cystic lesion with septum in the left thyroid and multiple small cystic lesions in the right thyroid. Lymph node swelling of the cervical region, supraclavicular fossa and submandibular region was also observed. Left thyroidectomy and lymph node dissection were performed. Histologically, cysts were lined by stratified squamous epithelium and dense lymphoid tissue having conspicuous follicle formation surrounded the epithelial lining. Solid cell nest (SCN)-like aggregations were seen in the thyroid parenchyma adjacent to the cyst walls and a small number of thyroid follicles were observed in the fibrous wall. Immunohistochemically, it is suggested that both the cyst lining and SCN-like aggregations are originally from thyroid follicles. Although, the exact histogenesis of branchial cleft-like cysts remains unclear, there are probably two different processes for its development, one is of branchial cleft origin and the other is mere squamous metaplasia, while in our case the latter is suggested. Herein, we report our new case and update information about branchial cleft-like cysts that appears in the literature.