Background: Cohort studies have examined whether change in transport mode is associated with change in bodyweight among commuters. We complement this research by examining trends in body mass index (BMI) for men and women who used the same transport mode between 2007 and 2013, and where transport was used for any activity of daily life. Methods: Data are from the HABITAT study, a longitudinal investigation of health among 11,035 persons aged 40–65 residing in 200 neighbourhoods in Brisbane, Australia. Transport mode was measured as private motor vehicle (PMV), public transport, walking, and cycling. Analyses were conducted using random effects models before and after adjustment for time-varying and time-invariant confounders. Interactions between transport mode and time were modelled to assess whether the rate of change in BMI differed by mode. Results: Averaged over the four time-points, the BMI of men who consistently walked or cycled was −3.20 kg/m2 (95%CI −4.28, −2.12) and −2.15 kg/m2 (95%CI −3.22, −1.08) lower respectively than PMV users: the corresponding difference for women who walked or cycled was −2.42 kg/m2 (95%CI −3.66, −1.18) and −2.44 kg/m2 (95%CI −5.98, 1.11). For men, there were no BMI differences between PMV and public transport users; among women, those who mainly used public transport had higher BMI (1.06 kg/m2 95%CI 0.51, 1.62) than PMV users. For men, no significant interactions were found between transport mode and time; for women, those who mainly walked for transport experienced a significant decline in BMI compared with PMV users. Conclusion: Those who consistently walked or cycled sustained a lower BMI over time relative to those who consistently used a PMV. Transport and land use policies and behavioural interventions that successfully shift mode-share from PMV to active travel might help stem the global increase in obesity related chronic disease.