Mucociliary clearance represents a host defense mechanism of airways that can be compromised by various pathologic conditions, such as nasal septal deviation. Although septoplasty can resolve obstruction, it impairs mucociliary clearance in the immediate postoperative period. Clinical studies have demonstrated how hyaluronic acid can interfere with this function. Our study aims to provide evidence of a therapeutic effect of hyaluronic acid on nasal mucosa recovery after septoplasy. Sixty-five patients underwent septoplasty. On postoperative day 1, patients were randomized to a control arm that was treated with mupirocin ointment or an experimental arm that received additional treatment with sodium hyaluronate solution. Pre- and postoperatively, anterior rhinoscopy was performed to analyze mucosal status, and mucociliary clearance was measured by using the saccharin transit time (STT) method. The t test was used for independent groups. During the preoperative evaluation, we observed a significant difference in STT between the convex and concave side in both groups. Fifteen days after surgery, we observed a significant difference preoperatively to postoperatively for both the convex and the concave side (p < 0.02 and p < 0.008, respectively). One month after surgery, we observed a reduction of STT when comparing preoperative control group values and, after 1 month, postoperative values in both sides (p < 0.015 and p < 0.005, convex and concave side, respectively). Our results show a significant reduction of the STT for both nasal sides as soon as 15 days after septoplasty in patients randomized to additional treatment. Our experience provides further evidence for the therapeutic effect of hyaluronic acid in accelerating nasal mucosa recovery after septoplasty.