Aim: to evaluate the outcome of endoscopic technique for treating choanal atresia (CA) cases as well as to compare it with that of transnasal puncture. Methods: A retrospective cohort study was performed at the Otolaryngology-Head Neck Surgery department, King Abdulaziz University Hospital, Jeddah, KSA during the period between 2010-2017. Results: The type of first operation (endoscopic or transnasal puncture) was shown to have a significant relation to the restenosis rate after the first operation (P=0.02), where initial puncture repair had less restenosis rate. On the other hand, there was no significant difference between the two surgical techniques regarding the duration between the first and second operations (p-value=0.064), the required stenting period postoperatively (p-value=0.934), nor the total number of required operations (p-value=0.206). The use of Mitomycin, stents and decongestants had no significant effect on restenosis rate (p-values=0.515, 1.00 and 0.838 respectively). Conclusion: Endoscopic transnasal choanal atresia repair technique did not prove to be superior to older puncture technique. Stenting had no significant effect on repair outcome. Mitomycin C had somewhat a positive effect on prolonging restenosis. We believe that a transoral endoscopic approach might be superior technique to current transnal technique.