Background: The effects of infection and developmental adaptations in infancy on the prevalence of subsequent atopy-related diseases at different ages during childhood are not fully determined. This study aims to examine the similarities and differences in the age-specific association of asthma, allergic rhinitis/conjunctivitis, and atopic dermatitis with early life infection (i.e., daycare, older siblings, and severe airway infection) and developmental adaptations (i.e., preterm birth and overweight gain) in children. Methods: In this longitudinal cohort study (n = 47,015), children were followed from 0.5 to 11 years. The potential risks and protective factors, including daycare attendance at 0.5 years, existence of older siblings, history of hospitalization due to cold/bronchitis/bronchiolitis/pneumonia during 0.5–1.5 years, preterm birth, and overweight gain at 1.5 years, were assessed using multivariable logistic regression with adjustments for potential confounders. Results: A negative association was observed between early life daycare attendance and asthma at 5.5–9 years, which disappeared after 10 years. A negative association was also noted throughout childhood between early life daycare attendance and the presence of older siblings with allergic rhinitis/conjunctivitis. However, the association between early daycare and atopic dermatitis was found to be positive during childhood. In contrast, the early life history of hospitalization owing to cold/bronchitis/bronchiolitis/pneumonia was identified to be a risk factor for developing both asthma and allergic rhinitis/conjunctivitis. Preterm birth was a significant risk factor for childhood asthma. Conclusion: Different age-specific patterns were demonstrated in the relationship between early life daycare, severe airway infection, preterm birth, and atopy-related diseases in childhood.