Microbial fuel cells (MFCs) pertain to a kind of modern technology for the direct conversion of chemical energy in organic matter from wastewaters into electricity during the oxidation of organic substrates. A system of continuous MFC was constructed for the treatment of real petroleum refinery wastewater (PRW). The treatment of real PRW, operational performance of the MFC system, biodegradation of furfural, and energy output were investigated in this study. The MFC was inoculated by mixed anaerobic bacteria, with Bacillus sp. as the dominant type, and continuously operated for 30 days. The biodegradation of furfural and phenol, which are the most prevalent toxicants in refinery wastewater, was investigated. The MFC system reached maximum energy outputs of 552.25 mW/m3 and 235 mV. In the anodic chamber, the maximum removal of furfural and phenol was higher than 99%, with biodegradation of organic content reaching up to 95%. This study demonstrated the viability of a continuous-flow MFC system as a green technology for the treatment of furfural-rich real refinery effluents while generating electricity.