Our study aimed to compare the efficacy, safety, and clinical effect of the transoral approach and the bilateral areolar approach (BAA) for endoscopic thyroglossal duct cyst (TGDC) resection. In total, 42 patients who received an endoscopic TGDC resection between January 2019 and May 2022 via a transoral (n = 22) or bilateral areolar (n = 20) approach by a single surgeon were retrospectively enrolled. We collected and compared the following data: patients' demographic data, complication events, operative time, bleeding volume, drainage volume, 6-h postoperative pain scores, length of hospitalisation, resected TGDC size, and cosmetic satisfaction. There were no cases of conversion to a transcervical approach in the two groups. No significant differences were found between the two groups in terms of age, sex, body mass index, complication, bleeding volume, 6-h postoperative pain scores, and TGDC size (all p > 0.05). However, the operative time and patients' cosmetic satisfaction were higher in the transoral group than in the BAA group (all p < 0.05). In addition, the drainage volume and length of hospitalisation in the transoral group were less than those in the BAA group (all p < 0.05). Both the transoral approach and BAA are safe and reliable; however, the transoral approach is more complex than the BAA and offers better cosmetic satisfaction. Doctors should choose the appropriate surgical procedure based on the patient's condition and preferences.