Objectives Endoscopic techniques in pituitary surgery lead to inevitable mucosal loss of the sphenoethmoidal recess and posterior nasal septum in the nasal cavity. There is no other comparative study between primary reconstruction of septal perforation and secondary healing in the literature. The aim of this study is to evaluate postoperative patient morbidity with or without posterior septal perforation in endonasal pituitary surgery by comparing two commonly used techniques: rescue and double nasoseptal flaps. Design Prospectively randomized study. Setting Tertiary academic center. Participants Sixty patients underwent endoscopic endonasal pituitary surgery. Main Outcomes and Measures Functional results (breathing) using visual analog scale (VAS), sphenoid sinusitis, presence of synechia, perforation in the posterior septum, and crusting in the sphenoethmoidal recess were assessed. Results Pre- and postoperative mean VAS scores were 71.67 +/- 11.47 and 67.67 +/- 9.71 mm in the intact septum group and 77.67 +/- 14.06 and 62.67 +/- 10.48 mm in the posterior septal perforation group. There was a significant difference between pre- and postoperative VAS values in all groups. There was significant worsening in both groups; worsening in VAS values was much higher in the posterior septal perforation group. In the posterior septal perforation group, much more crusting was seen. Conclusions This is the first study to compare the postoperative patient morbidity in endoscopic endonasal pituitary surgery with and without a posterior septal perforation. Reconstruction of the posterior septum along with less mucosal loss yields better postoperative nasal symptom score.