Objectives <p>The aim of the current study was to evaluate the functional sinonasal outcomes after rescue flap versus double nasoseptal flap in endoscopic endonasal pituitary surgery.</p> Methods <p>This randomized clinical trial was conducted over 1.5 years over 60 patients who underwent endoscopic trans-sphenoid surgery for macroadenomas (more than 2&#xa0;cm.). the patients were randomly allocated into 2 groups: the rescue flap group, (<i>n</i> = 30) and the double nasoseptal flap group (<i>n</i> = 30). Functional sinonasal outcomes were evaluated in both groups in terms of sinonasal outcome test (SNOT-22), crusting, adhesions, and olfaction.</p> Results <p>the sinonasal outcome test (SNOT-22), as well as the olfaction scores were significantly better in the double flap group compared to the rescue flap group. Crusting and adhesions occurred more frequently in the rescue flap group. The nasal stage operative time was significantly longer in the double flap group than the rescue flap group.</p> Conclusion <p>Endoscopic pituitary surgery can adversely affect the sinonasal functions. Double nasoseptal flap technique allows posterior septectomy with bilateral septal mucosa preservation. Although it requires longer operative time than the rescue flap technique, better functional sinonasal outcomes and olfaction scores are achieved.</p>