Background: Mucociliary clearance is one of the most important protective functions of the airway. Previous studies, checking the influence of allergic rhinitis (AR) on mucociliary clearance time (MCT), were made on small patient groups and brought contradictive results. Objectives: The aim of the study is to confirm whether AR in children influences MCT. Methods: The examined group consisted of 842 AR children. A total of 96 children with no history of allergy rhinitis served as a comparative group. All patients underwent saccharin and skin prick tests and tests for blood eosinophilia, nasal eosinophilia, vitamin D3 serum concentration, total and specific IgE serum concentration. Results: Nasal MCT was significantly longer in AR patients (mean ± SD: 10.5 ± 5.65 min) compared to controls (mean ± SD: 7.25 ± 4.3 min). Percentage of eosinophils in nasal smears in patients was significantly higher compared to controls and a weak, but significant positive correlation was observed between the percentage and MCT (r > 0.10, p < 0.008). Patients with intermittent and persistent moderate/ severe AR had significantly longer MCT and higher eosinophilia in nasal smears compared both to patients with intermittent and persistent mild RA and controls. No correlation was observed between MCT and: participant’s age, total serum IgE, vitamin D3 serum concentration, absolute number or percentage of eosinophils in blood, prick test results or duration of illness. Conclusions: AR affects the mucociliary clearance in children, and its deterioration is related to more severe rhinitis with higher intensity of local nasal inflammation, reflected in nasal smear eosinophilia.