Abstract Background Studies investigating whether respiratory syncytial virus (RSV) infection, non‐RSV respiratory infections, respiratory‐related disorders, and non‐respiratory‐related disorders are associated with subsequent wheezing are limited in Japan. We aimed to elucidate the relationship between hospitalization for RSV infection, non‐RSV respiratory infections, respiratory‐related disorders, as well as non‐respiratory‐related disorders and subsequence wheezing in Japanese children. Methods This study included 7340 children and was conducted under the TMM BirThree Cohort Study (Tohoku Medical Megabank Project Birth and Three‐Generation Cohort Study). Data was collected from birth records and questionnaires. We categorized hospitalization history into five categories: “no hospitalization,” hospitalizations for “RSV infection,” “non‐RSV respiratory infections,” “respiratory‐related disorders,” and “non‐respiratory‐related disorders.” The association of the five categories with later wheezing at 3 years of age was evaluated using multivariable logistic regression analysis. Results After adjusting for covariates, an association was shown between hospitalization under 2 years of age and later wheezing (odds ratio [OR] = 2.78; 95% confidence interval [CI] = 1.97–3.88 for “RSV infection”; OR = 2.61; 95% CI = 1.44–4.57 for “non‐RSV respiratory infections”; and OR = 3.33; 95% CI = 2.43–4.54 for “respiratory‐related disorders”). Conclusion Hospitalization of children under 2 years of age for RSV infection as well as non‐RSV respiratory infections and respiratory‐related disorders were associated with subsequent wheezing.