Lymphangioma is a rare benign congenital tumor of the lymphatic system, which is commonly diagnosed before 2 years of age. In the natronal report, cystic lymphangioma was usually reported as a huge translucent mass located in the head and neck area. It's occurrence in retropharyngeal space with respiratory obstruction and swallowing difficulty in neonate is extremely rare and postoperative nasopharyngeal reflux has rarely been reported. Complete resection is the standard therapy. However, involvement of the upper airway may be determining prognosis in the extensive lymphangiomas because of the difficulty of complete excision. We present a case of cystic lymphangioma in neonate which was initially asymptomatic but gradually progressed to cause respiratory obstruction due to enlargement. After resection, nasopharyngeal reflux developed with dysfunction of the soft palate and gradually improved with conservative care over 5 months.