Physical activity (PA) can have a positive influence on mental health. Less is known about the influence of mental health on current and later PA and sedentariness in childhood. This study investigated cross-sectional and distal associations between behavioural and emotional development, and objectively measured moderate-to-vigorous PA (MVPA) and sedentary time, in seven-year-old children participating in the Millennium Cohort Study (n = 6,497). Markers of behavioural/emotional development (scores for total difficulties, internalising and externalising problems) were obtained using the Strengths and Difficulties Questionnaire at ages three, five and seven years. Associations between sedentary time or MVPA (outcomes) and behavioural/emotional development (exposures) were analysed using median regressions, stratified by sex. In cross-sectional analyses, boys’ sedentary time decreased with higher total difficulties scores (-1.1 minutes/day per score unit), boys’ and girls’ sedentary time decreased with higher externalising scores (-2.3 minutes/day per unit), and girls with higher internalising scores were more sedentary (1.4 minutes/day per unit). In analyses of MVPA, boys and girls were marginally more active with higher externalising scores (0.4 and 0.5 minutes/day per unit), and boys were less active for higher internalising scores (-0.7 minutes/day per unit). Distal associations showed similar patterns: children with increasing total difficulty and externalising scores at all ages were less sedentary at age seven; girls with increasing internalising scores particularly so. Boys and girls with increasing externalising scores were more active at age seven, whilst increasing internalising scores reduced MVPA for boys. In conclusion, behavioural/emotional development is associated with mid-childhood sedentary time and, more weakly, MVPA; this is of relevance to public health interventions aimed at increasing activity levels and the wellbeing of our young people.