Limitations have arisen when measuring associations between the neighbourhood social environment and physical activity, including same-source bias, and the reliability of aggregated neighbourhood-level social environment measures. This study examines cross-sectional associations between the neighbourhood social environment (perceptions of incivilities, crime, and social cohesion) and self-reported physical activity, while accounting for same-source bias and reliability of neighbourhood-level exposure measures, using data from a large population-based clustered sample. This investigation included 11,035 residents aged 40–65 years from 200 neighbourhoods in Brisbane, Australia, in 2007. Respondents self-reported their physical activity and perceptions of the social environment (neighbourhood incivilities, crime and safety, and social cohesion). Models were adjusted for individual-level education, occupation, and household income, and neighbourhood disadvantage. Exposure measures were generated via split clusters and an empirical Bayes estimation procedure. Data were analysed in 2016 using multilevel multinomial logistic regression. Residents of neighbourhoods with the highest incivilities and crime, and lowest social cohesion were reference categories. Individuals were more likely to be in the higher physical activity categories if they were in neighbourhoods with the lowest incivilities and the lowest crime. No associations were found between social cohesion and physical activity. This study provides a basis from which to gain a clearer understanding of the relationship between the neighbourhood social environment and individual physical activity. Further work is required to explore the pathways between perceptions of the neighbourhood social environment and physical activity.