Pollen food allergy syndrome (PFAS) is caused by cross-reactivity with pollen; however, not all-pollen-sensitised individuals develop PFAS, and studies on the characteristics of PFAS development are limited in Japan. We investigated the prevalence and risk factors for the development of PFAS in Japanese children and adolescents sensitised to pollen and their association with pollen-specific IgE levels. The characteristics of PFAS were investigated in patients with allergies aged 3–18 years who visited Dokkyo Medical University Hospital between January 2016 and December 2019. Specific IgE levels for alder, Japanese cedar, ragweed, and orchard grass were measured in patients sensitised to any of the pollens. Patients were categorised into preschool (G1), elementary school (G2), and middle-high school (G3) groups. Overall, 600 patients were enrolled. The prevalence of PFAS was 8.5% in G1, 20% in G2, and 36.3% in G3. Multivariate logistic regression analysis demonstrated strong associations between the risk of developing PFAS and older age (odds ratio (OR), 1.12; 95% confidence interval (CI), 1.06–1.19; P