Hairy polyps of the head and neck are rare congenital tumors that may cause upper aerodigestive tract impairment in newborn. Although cleft palate is a common congenital anomaly, hairy polyp with cleft palate is extremely rare in the newborn. We aimed to present the planning of reconstruction in a patient who has an incomplete cleft palate and defect due to hairy polyp excision on soft palate in this report. A 9-month-old child was admitted to our clinic due to cleft palate. In the clinical examination, incomplete cleft palate plus a defect on the posterior side of the left soft palate was observed. On the history, the patient had been operated urgently at the newborn period for a hairy polyp localized on the left soft palate which had obstructed the airway. Wardill-Kilner-Veau technique was modified for the reconstruction of the defect on the soft palate and incomplete cleft palate. No complication was seen on postoperative period. The speech ability was evaluated on the late postoperative controls after 3 years and adequate speech intelligibility was obtained. A case of hairy polyp of nasopharynx with incomplete cleft palate in a neonate and its reconstruction techniques are discussed. The etiology of hairy polyp, hamartoma, teratoma, dermoid cyst and epignathus, their nomenclature, histopathology, clinical features, and management in neonates are also discussed briefly.