Microbial fuel cell (MFC) and its cathode performances were compared with use of carbon fiber brush and plain carbon paper cathode electrodes in algae aeration. The MFC having carbon fiber brush cathode exhibited a voltage of 0.21 ± 0.01 V (1,000 Ω) with a cathode potential of around −0.14 ± 0.01 V in algal aeration, whereas MFC with plain carbon paper cathode resulted in a voltage of 0.06 ± 0.005 V with a cathode potential of −0.39 ± 0.01 V. During polarizations, MFC equipped with carbon fiber brush cathode showed a maximum power density of 30 mW/m2, whereas the MFC equipped with plain carbon paper showed a power density of 4.6 mW/m2. In algae aeration, the internal resistance with carbon fiber brush cathode was 804 Ω and with plain carbon paper it was 1,210 Ω. The peak currents of MFC operation with carbon fiber brush and plain carbon paper cathodes were −31 mA and −850 µA, respectively.