Purpose: Thyroglossal duct cysts (TGDCs) may cause cosmetic defects or more serious impairments if left untreated. Our study was designed to examine the potential advantage of endoscopic surgery performed on TGDCs, especially the ability to completely resect the branches and to affect the cosmetic appearance. Patients and Methods: Thirty-two patients from Beijing Tongren Hospital, Beijing, China, diagnosed with TGDCs were selected. Seventeen patients with TGDCs underwent traditional Sistrunk's surgery, and 15 patients underwent endoscopic cystectomy. Results: All patients had complete resection and were followed up from 6 months to 4 years. None had a recurrence after endoscopic resection. However, patients in the traditional surgery group had a 5.9% (1/17) rate of recurrence. The incision length was approximately 2.1 cm in the endoscopic group compared with 5.2 cm in the traditional group. The mean time for the endoscopic operation was 97.7 minutes compared with 51.6 minutes in the traditional surgical procedure. The average length of hospital stay was 6.7 days in the endoscopic group compared with 9.7 days in the traditional group. Conclusions: Endoscope-assisted small-incision thyroglossal duct cystectomy is an efficient method. It causes fewer cosmetic defects and also decreases operative time. It will likely become the new standard procedure for patients with TGDCs.