Background Finding associated factors with childhood behavioural problems as early as preschool age is important. Studies have revealed several factors including socioeconomic factors, which may vary among different cultural background and population. However, investigation in general Japanese population of preschool age has not been well demonstrated. Thus, the objective of this study was to examine associated factors of childhood behavioural problems using Strengths and Difficulties Questionnaire (SDQ) in a prospective birth cohort study. Methods Total 3813 SDQ were distributed between October 2014 and December 2015 to the subpopulation of prospective birth cohort study, the Hokkaido Study on Environment and Children's Health. The subpopulation consisted of participants who had reached age 5 and were born between April 2008 and December 2010. Baseline questionnaire filled at recruitment and birth record were used to obtain participant information. Children with total difficulties score ≧ 13 were defined as likelihood of behavioural problems. A total of 2553 children with valid answers were included into the analysis. The response rate was 67.1%. Results Number of children with likelihood of behavioural problems was 521 (20.4%). Boys showed more problematic scores than girls. Multivariate analysis found that maternal pre‐pregnancy BMI ≧ 30 kg/m2, primipara, maternal education lower than high school, family income during pregnancy < 3 million yen/year and boy gender were the factors associated with increased odds ratio of likelihood of child behavioural problems. Conclusions This study found that prenatal socioeconomic factors were associated with likelihood of child behavioural problems at preschool age in Japan.