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This study aimed to evaluate the long-term outcomes of endonasal surgical treatment for choanal atresia (CA) and determine possible predictors of recurrence. A retrospective study of 50 cases of CA that were managed endonasally was conducted at an academic tertiary referral centre. Recurrence of disease was assessed with regard to the type and nature of atresia, presence of CHARGE association and stent usage. Bilateral CA cases (n = 76 sides) were operated at an early age and had an incidence of recurrence of 57%, while unilateral cases had a recurrence rate of 25% (3/12). Use of stents did not have a statistically significant effect on the rate of recurrence. However, a significantly higher recurrence rate was noted in patients with purely bony atretic plates (p < 0.001) or CHARGE association (p = 0.049). A tendency towards a higher recurrence rate in bilateral atresias was also found (p = 0.085). The transnasal approach is a safe and effective way to re-establish the nasal choanae. However, appropriate information on the likelihood of recurrence should be included in the preoperative counselling of patients and their parents, especially in cases with bilateral atresia or CHARGE association.