Modular construction has attracted increasing attention due to its energy and environmental benefits. Digital technologies such as building information modelling (BIM) have also been explored to generate and manage data through the lifecycle of buildings. Although research has been performed in the area of integrating BIM and modular construction, BIM-based automated lifecycle assessment (LCA) of prefabricated buildings remains unexplored. This study therefore aims to develop a BIM-based LCA method for prefabricated buildings incorporating different assessment levels with unique system boundaries and functional units. The developed approach can support automated assessments through all lifecycle phases of a prefabricated building. It is achieved through an automated process of creating parameters to merge LCA data into the building model, systematic zoning, model setup and impact estimation. This approach is applied to evaluate the energy and environmental performances of a case building in Hong Kong. The case study validated the efficiency of the developed BIM-based LCA method in providing a systematic and detailed assessment of modularly designed buildings. This study extends the knowledge in automated BIM-based LCA by addressing specific characteristics of prefabrication and promotes the incorporation of comprehensive and detailed LCA data into BIM models for improved design robustness and holistic performances of buildings. This validated approach will enhance the willingness of designers to apply LCA during the design stages for minimizing the energy and environmental impacts of both new and renovated buildings with prefabrication.