The phyto-Fenton process, which generates hydroxyl radicals through Fenton and Fenton-like reactions using plant-derived hydrogen peroxide (H2O2) and ferrous iron (Fe (II)) can degrade organic pollutants. Duckweed, an aquatic plant, is promising for a co-beneficial phytoremediation process that combines wastewater treatment and biomass production for biofuel feedstock. However, the phyto-Fenton process using duckweed has not been extensively studied. Because sulfamethoxazole (SMX), a major antibiotic, is distributed widely and is an emerging contaminant, its effective removal from contaminated water is necessary. The present study investigated the possibility of the simultaneous efficient removal of SMX from polluted water and biomass production for fuel feedstock by the phyto-Fenton process using duckweed. This is the first attempt to demonstrate the co-benefits of SMX removal and biomass production using duckweed. Intracellular H2O2 was produced using four duckweeds, Lemna aequinoctialis, L. minor, Landolina punctata, and Spirodela polyrhiza, in the range of 16.7–24.6 μ mol g−1 fresh weight, and extracellular H2O2 was released into the water phase. Consequently, duckweed could be used as an H2O2 supply source for the phyto-Fenton process. Specifically, 0.5 g fresh duckweed almost completely eliminated 1 mg L−1 SMX after 5 d in 50 mL sterile modified Hoagland solution containing 10 mM Fe (II). Fe (II)-dependent elimination of SMX indicated the occurrence of phyto-Fenton reaction. The phyto-Fenton process using duckweed effectively removed SMX. S. polyrhiza duckweed similarly removed 1 mg L−1 SMX even in sewage effluent containing other organic contaminants. During this treatment, duckweed biomass was generated at 7.95 g dry weight m−2 d−1, which was converted into methane at 353 normal liters CH4 kg−1 volatile solids by anaerobic digestion. For the first time, this study clearly demonstrates the potential for simultaneous SMX removal and biomass production from SMX-contaminated wastewater using duckweed. Display omitted •Duckweed produced H2O2 and released it to water phase.•Duckweed supplied enough H2O2 for the phyto-Fenton process.•Sulfamethoxazole (SMX) was efficiently removed by the phyto-Fenton process.•Duckweed biomass (7.95 g-dry weight) m−2 d−1 was produced during SMX removal.•Duckweed biomass was converted to 353 NL methane kg−1 volatile solids.