The aim of this study was to examine how family structure is associated with moderate-to-vigorous-intensity physical activity (MVPA) for children aged between 6 and 11. At 6, 9 and 11 years, children wore an accelerometer and parents/carers completed questionnaires on demographics and family structure. Linear regression models examined cross-sectional associations between family structure and MVPA at age 9 and 11. Linear multilevel models examined longitudinal associations between age 6 and 11, differences in change over time were examined using interaction terms. No associations between exposures and MVPA were evident at age 9. Compared to boys living in one home, eleven-year-old boys who lived in multiple homes performed 15.99 (2.46–29.52) fewer minutes of MVPA on weekend days. In longitudinal analyses, the evidence was unclear whether the association with family structure changed over time. Models that assumed associations with family structure remained constant over time, found that boys who lived in multiple homes performed 11.02 (0.76–21.28) fewer minutes of MVPA per weekend day, while for each additional sibling, girls performed an extra 1.89 (0.25–3.53) minutes of MVPA per weekend day. Findings indicate a small number of associations, varying in magnitude, between family structure and children’s MVPA. Therefore, families of all structures should be supported to help their children meet MVPA recommendations.