Ciprofloxacin-containing saline wastewater treatment gains increasing attentions, due to the problems of limited degradation and spreading risk of antibiotic-resistance genes (ARGs). Sulfate reduction is a cost-efficient technology for simultaneous sulfate and antibiotic removal. The microbial fuel cell enhances removal of antibiotics and reduces spreading risk of ARGs in effluents, however, the biotransformation of ciprofloxacin (CIP) in sulfate-reducing microbial fuel cell (SR-MFC) remains unclear. Thus, a SR-MFC is established in this study for treatment of CIP-containing saline wastewater, which achieves simultaneous removal of CIP (50.2%), sulfate (85.1%), and ARGs (17.0%). The Desulfovibrio sp. bacteria become dominant in free biomass (58.8%) and biofilm (73.6%) after CIP exposing, respectively. The CIP can be utilized in prior to lactate for sulfate reduction, while the energy production is initially contributed to sulfate reduction followed by sulfide oxidation. Notably, the expression of ARGs declines probably due to enhanced biotransformation and limited adsorption (2.6%) of CIP on biomass after CIP addition. Long-term exposure to CIP enriches the ARGs of antibiotic efflux pump, implying some CIP is pumped out from intracellular to extracellular. A novel degradation pathway attacking the N15 site in piperazine may be the major and environmental-friendly biotransformation reaction, where the enzyme of ammonia-lyase and acetyltransferase are involved in. To our best knowledge, this is the first report of the novel pathway in bacterial CIP degradation system, which is known as fungal CIP biotransformation pathway. This study provides insights for CIP biotransformation in SR-MFC, and the operational strategy for antibiotic-containing saline wastewater treatment with ARGs control.