Purpose The aim of this study was to reveal the effect of N95 and surgical masks on mucociliary clearance function and sinonasal complaints. Methods Sixty participants were enrolled in this study, including 30 people in N95 mask group and 30 people in surgical mask group. Two interviews, three days apart, were performed with all participants. The participants were asked not to use any mask before the first interview while they were asked to use the determined mask just before the second interview for 8 h. In both interviews, the mucociliary clearance times (MCTs) were measured and participants were asked to score ten distinct sinonasal complaints using visual analog scale (VAS). Data obtained from first interview were named pre-mask data, data obtained from second interview were called after-mask data. In both groups, pre-mask MCTs and VAS scores were compared with after-mask MCTs and VAS scores. Results After-mask MCTs (mean = 13.03 +/- 6.05 min) were significantly longer than pre-mask MCTs (mean = 10.19 +/- 4.21 min) in N95 mask group (p = 0.002). No significant difference was found between after-mask and pre-mask MCTs (mean = 12.05 +/- 5.21 min, mean = 11.00 +/- 5.44 min, respectively) in surgical mask group (p = 0.234). When after-mask VAS scores were compared with pre-mask VAS scores, it was found that N95 mask use increased nasal blockage and postnasal discharge, surgical mask usage increased nasal blockage. Conclusion While the use of N95 mask leads to nasal blockage and postnasal discharge, surgical mask use results in nasal blockage. N95 masks cause impairment in mucociliary clearance function. But all these effects are mild. Surgical masks have not been found to have any effect on mucociliary clearance function.