Background: Administration of factor IX (FIX) is the first-line treatment of hemophilia B patients and its large-scale production is of great importance to meet the needs of these patients. Therefore, this study aimed to evaluate the expression and secretion efficiency of rFIX produced by S2 cells and compare it with human embryonic kidney (HEK) cells. Methods: Escherichiacoli strain DH5α was used to amplify pcDNA/FIX and pMT/FIX plasmids. After plasmid isolation, HEK and S2 cells were transfected to express rFIX. rFIX activity was measured using a coagulation activity assay. Furthermore, rFIX expression level in the transfected cells was measured using an ELISA technique. Results: The findings of this study indicated that the rFIX expression in both transfected S2 and HEK cells and both cells showed coagulation activity. Although, HEK cells showed higher rFIX secretion efficiency compared to S2 cells, hFIX-transfected S2 cells had higher rFIX expression level compared to HEK ones. Conclusion: Overall, it was concluded that S2 cells are a more suitable option for large-scale production of rFIX due to their ability to express high level of this coagulation factor.