The biocathode in a microbial fuel cell (MFC) system is a promising and a cheap alternative method to improve cathode reaction performance. This study aims to identify the effect of the electrode combination between non-chemical modified stainless steel (SS) and graphite fibre brush (GFB) for constructing bio-electrodes in an MFC. In this study, the MFC had two chambers, separated by a cation exchange membrane, and underwent a total of four different treatments with different electrode arrangements (anodeǁcathode)—SSǁSS (control), GFBǁSS, GFBǁGFB and SSǁGFB. Both electrodes were heat-treated to improve surface oxidation. On the 20th day of the operation, the GFBǁGFB arrangement generated the highest power density, up to 3.03 W/m3 (177 A/m3), followed by the SSǁGFB (0.0106 W/m3, 0.412 A/m3), the GFBǁSS (0.0283 W/m3, 17.1 A/m3), and the SSǁSS arrangements (0.0069 W/m−3, 1.64 A/m3). The GFBǁGFB had the lowest internal resistance (0.2 kΩ), corresponding to the highest power output. The other electrode arrangements, SSǁGFB, GFBǁSS, and SSǁSS, showed very high internal resistance (82 kΩ, 2.1 kΩ and 18 kΩ, respectively) due to the low proton and electron movement activity in the MFC systems. The results show that GFB materials can be used as anode and cathode in a fully biotic MFC system.