ObjectivesTo examine the prevalence of socioemotional and behavioural difficulties (SEBDs) in children with chronic physical conditions (CPCs) and to analyse how this prevalence varied with the type and number of CPCs and the age of the child.DesignCross-sectional study of a secondary data analysis of the Longitudinal Study of Australian Children.SettingAn Australian nationally representative sample of general population of children.Participants15 610 children-waves aged 6–14 years.Intervention/exposureChildren reported to have at least 1 of the 21 CPCs by their parents.Main outcome measuresClinically relevant SEBDs were defined using standardised cut-offs of the parent-administered Strengths and Difficulties Questionnaire.ResultsChildren with a CPC have significantly increased odds of total, internalising and externalising SEBDs than those without (total SEBDs, adjusted odds rartio or OR 3.13, 95% CI 2.52 to 3.89), controlling for sex, age, socioeconomic status and parental mental health status. The highest prevalence of total SEBDs was found in children with chronic fatigue (43.8%), epilepsy (33.8%) and day wetting (31.6%). An increasing number of comorbid CPCs was associated with a rising prevalence of SEBDs. On average, 24.2% of children with at least four CPCs had SEBDs. These children had 8.83-fold increased odds (95% CI 6.9 to 11.31) of total SEBDs compared with children without a CPC. Age was positively related to the odds of SEBDs.ConclusionChildren with a CPC have a significantly increased risk of having SEBDs than those without. These findings highlight the need for routine assessment and integrated intervention for SEBDs among children with CPCs.