Background <p>Allergic rhinitis (AR) is a common condition affecting 23% of children in Europe. Of the AR-patients, 40–72% do not follow the treatment instructions as provided by their clinician. Shared decision making is effective in improving adherence to treatment. Knowing treatment preferences of children and adolescents can help improve shared decision making.</p> Objective <p>To determine the preferential treatment of children and adolescents with AR.</p> Methods <p>This study is a secondary analysis. Data from a single-blinded randomized controlled trial were used. The primary outcome measure of the original study was percentage of symptom-free days. Children aged 6–18 were randomised in three treatment groups: antihistamines (AH) on-demand, intranasal corticosteroids (INCS) continuous or INCS on-demand. Preferences were mapped out by questionnaires at the start and end of the study. The study design was approved by the Ethical Review Board of the Erasmus MC University Medical Center Rotterdam (No. MEC-2012-354). Prior to performing the trial, it was registered (Netherlands Trial Register No. NL3276).</p> Results <p>At the end of the study AH on-demand was the preferential treatment arm (54.7%, <i>N</i> = 76/139). Preferences for continuous use over on-demand use and intranasal over oral therapy were dependent of treatment group (<i>p</i> = 0.027, <i>p</i> = 0.004). Of the participants, 36.7% chose their study medication as preferential treatment. Adolescents had more distinct treatment preferences than children (<i>p</i> = 0.004). Of the adolescents, 63% preferred AH on demand (<i>P</i> = 0.005), whereas children did not show a significant preference.</p> Conclusion <p>There is a significant difference in preferences for treatment for AR between children and adolescents. AH on-demand is the most preferred medication type for AR. Shared decision making in choosing AR treatment should be used to improve the treatment compliance.</p>