Objectives (1) To investigate differences in health-related, home and neighbourhood environmental variables between Liverpool children living in areas of high deprivation (HD) and medium-to-high deprivation (MD) and (2) to assess associations between these perceived home and neighbourhood environments and health-related variables stratified by deprivation group.Design Cross-sectional study.Setting 10 Liverpool primary schools in 2014.Participants 194 children aged 9–10 years.Main outcome measures Health-related variables (self-reported physical activity (PA) (Physical Activity Questionnaire for Older Children, PAQ-C), cardiorespiratory fitness, body mass index (BMI) z-scores, waist circumference), home environment variables: (garden/backyard access, independent mobility, screen-based media restrictions, bedroom media) and neighbourhood walkability (Neighbourhood Environment Walkability Scale for Youth, NEWS-Y).Explanatory measures Area deprivation.Results There were significant differences between HD and MD children's BMI z-scores (p<0.01), waist circumference (p<0.001) and cardiorespiratory fitness (p<0.01). HD children had significantly higher bedroom media availability (p<0.05) and independent mobility scores than MD children (p<0.05). MD children had significantly higher residential density and neighbourhood aesthetics scores, and lower crime safety, pedestrian and road traffic safety scores than HD children, all of which indicated higher walkability (p<0.01). HD children's BMI z-scores (β=−0.29, p<0.01) and waist circumferences (β=−0.27, p<0.01) were inversely associated with neighbourhood aesthetics. HD children's PA was negatively associated with bedroom media (β=−0.24, p<0.01), and MD children's PA was positively associated with independent mobility (β=0.25, p<0.01). MD children's independent mobility was inversely associated with crime safety (β=−0.28, p<0.01) and neighbourhood aesthetics (β=−0.24, p<0.05).Conclusions Children living in HD areas had the least favourable health-related variables and were exposed to home and neighbourhood environments that are unconducive to health-promoting behaviours. Less access to bedroom media equipment and greater independent mobility were strongly associated with higher PA in HD and MD children, respectively. Facilitating independent mobility and encouraging outdoor play may act as effective strategies to enhance PA levels and reduce sedentary time in primary school-aged children.