One of the important global challenges today is addressing the increasing demand for food while reducing its environmental impact. Sustainable intensification of rice-based cropping systems is a potential solution, but its environmental effect and sustainability in different intensive rice-based production systems have not been fully explored. Thus, in this study, we used the Life Cycle Assessment (LCA) to investigate the carbon footprint of three intensive rice-based cropping systems: rice-rice, rice-mungbean-rice, and maize-rice-rice. We analyzed the data generated from the International Rice Research Institute's ecological intensification platform project, implemented from 2013 to 2015. We included variables from essential farm inputs such as labor, fuel, machine use, water, seeds, fertilizers, and pesticide use in the LCA analysis. Grain yield, as well as the output of the three systems, were measured as well. Then, the carbon footprints generated by each system were calculated using conversion factors and constants available in published databases and articles. The results of this study can provide valuable information to design more sustainable rice-based cropping systems.