In pediatric individuals, polypharmacy would increase the prevalence of adverse drug reactions (ADRs). However, there is no report on the ADR increase adjusted for the influence of concomitant disease types. We conducted a retrospective study in pediatric patients to determine whether polypharmacy is a risk factor for ADR development, after the adjustment. Patients aged 1-14 years on medication who visited Gifu Municipal Hospital (Gifu, Japan) were included. We evaluated patient characteristics, ADR causality, ADR classification and severity, and ADR-causing drugs. We examined the association between ADR prevalence and number of drugs used. We performed multiple logistic regression analyses to investigate risk factors for ADR development. Of 1330 patients, 3.5% sought medical attention for ADRs. ADR causality was most often assessed as "possible," with gastrointestinal ADRs being the most common. Grade 1 ADRs were the most and antibiotics were the most common suspected ADR-inducing drug. The multiple logistic regression analysis showed that ≥ 2 or ≥ 4 drug use, neoplasms, mental and behavioral disorders, and circulatory system diseases significantly increased ADR prevalence. Polypharmacy increased the prevalence of ADR resulting in hospital visits in children, after adjusting for the influence of disease types. Therefore, proactive polypharmacy control measures are necessary for children.