The removal rate and degradation pathway of Sulfamethoxazole (SMX) in bioelectrochemical system (BES) and the elimination dynamics of SMX in a BES driven by stacked constructed wetland-coupled microbial fuel cells (CW-MFCs) were investigated. The results found that SMX (30 mg L−1) was rapidly degraded in the BES, and the SMX removal kinetics was simulated well by a first-order kinetic model (R2 > 0.93). Low current had no effect on the degradation products but enhanced the SMX removal rate. Biotransformation was the main pathway for the SMX elimination in the BES. The CW-MFCs supplied adequate and stable electricity (0.84–1.01 V) to support the BES for rapid SMX degradation without additional energy inputs. The relative abundance of Methanosarcina (18.7%) and VadinCA11 (3.1%) increased with an increase in voltage up to 1.2 V. However, the opposite was observed for Methanosaeta and Methanomassiliicoccus. The current in the BES influenced the methanogenic communities.