Introduction Otitis media (OM) and otitis media with effusion are commonly presenting conditions in an otolaryngology clinic. Exposure to passive smoking is thought to increase the risk of OM through an effect on mucociliary clearance, decreased ciliary beat frequency, or mucous hypersecretion. Awareness among parents plays a key role in the primary prevention of the disease. Objective We aimed to identify the association of passive smoking with OM among school-going children of the eastern region of Nepal. Methods A community-based cross-sectional study was done among 663 school-going children, selected by stratified random sampling using a questionnaire. Data regarding age, gender, type of school, otological symptoms, smoking status of parents and family members, otoscopic findings, pure tone audiometry, and impedance audiometry were recorded. Results Six-hundred and sixty-three students were included in the study. OM was confirmed in 103 students (15.5%). Smoking history was present in at least one of the family members in 177 out of 663 students (26.69%) and with positive smoking history in any member of the family, OM was seen in 65 (36.7%) students (p ≤ 0.001), which suggested significant association. OM was seen in 38 students (7.8%) when there was no exposure to passive smoking. Conclusions There is a high prevalence of OM (15.5%) in school-going children. The study shows significant association between passive smoking and OM in children.