Background: Choanal atresia and stenosis are the most common craniofacial abnormalities of the nose and often require more than one corrective surgery or can lead to life-threatening airway obstruction. Objectives: To evaluate the long-term outcomes of the endoscopic septonasal flap technique combined with silicone stents for the repair of congenital choanal atresia and to determine independent predictors of surgical success. Methods: This study was designed as a review of prospectively collected data. The study included 40 patients diagnosed with choanal atresia due to congenital nasal obstruction at our hospital's otolaryngology clinic. The demographic characteristics and hospital information of the cases were recorded. Patients with congenital choanal atresia were operated on using the endoscopic septonasal flap technique combined with silicone stents. The surgical results were evaluated. Results: Out of the 40 patients, 23 (57.5%) were female and 17 (42.5%) were male, with a mean age of 90 days, ranging from 2 days to 1650 days. The atretic plate was bilateral in 23 patients (57.5%) and unilateral in 17 (42.5%). The types of atresia among the cases were 14 (35%) bony, 17 (42.5%) membranous, and 9 (22.5%) mixed atresia. Postoperative restenosis developed in 7 (17.5%) of the cases. Revision was needed in 10% (n = 4) of the operated bilateral choanal atresia cases and 7.5% (n = 3) of the unilateral choanal atresia cases. In cases diagnosed with bilateral choanal atresia, oxygen need, malnutrition, follow-up time in the intensive care unit, and follow-up time in the ward were significantly longer (P < 0.05). Conclusions: The Septonasal flap technique combined with silicone stents may be effective in preventing potential complications and restenosis after surgery.