This research investigated the performance improvement of bioethanol-fuelled Solid Oxide Fuel Cell (SOFC) system with pervaporation. Two types of membrane, hydrophilic and hydrophobic were employed in a pervaporation integrated with SOFC system and their corresponding overall electrical efficiencies were compared. The results indicated that the system with hydrophobic membrane required much less thermal energy about 1/4 times and offered a higher overall electrical efficiency compared to the system with hydrophilic membrane. High ethanol separation factor values of hydrophobic membrane were required when the purification system was operated at higher ethanol recovery to achieve more overall efficiency. However, the real membranes which had high enough separation factor values of the hydrophobic type were limited. Afterwards, vapor permeation was proposed to be further installed after a hydrophobic pervaporation (hybrid vapor permeation-pervaporation) to solve the previous problem. Based on energy self-sufficient condition and PTMSP membrane regarded as the poorest separation performance, the simulation results showed that it could offer the overall electrical efficiency of about 2.4 times when installing a hydrophilic vapor permeation compared with the case of using the pervaporation alone. Among the different purification processes at base case, the overall electrical efficiency can be ranked by the following order: Hybrid vapor permeation-pervaporation > pervaporation > distillation column, respectively.