The firefly luciferase complementation assay is widely used as a bioluminescent reporter technology to detect protein-protein interactions in vitro and in vivo. Firefly luciferase oxidates its substrate, luciferin, resulting in the emission of light. A previous study suggests that the firefly luciferase complementation assay has different luminescence kinetics from full length luciferase. The mechanism behind this is still unknown. Although half of the previously published studies utilizing the firefly luciferase complementation assay consider it quantitative. To understand how the molecular reactions and the changes in the affinity of the protein pair affect experimental results, a mathematical model was constructed. This suggests that previously published studies should be considered qualitative, unless an additional experiment is performed. This new model demonstrates that the luminescence measured is not linearly correlated with the affinity of the protein pair. The model is then used to design a new experiment which allows the firefly luciferase complementation assay to be used quantitatively to detect changes of affinity.