A bench-scale experiment to cultivate rice for animal feeding with continuous irrigation of treated municipal wastewater (TWW) in six different conditions was carried out to examine nitrogen removal from TWW, yield and quality of harvested rice, and accumulation of heavy metals in soil and rice grains. A microbial fuel cell (MFC) system comprising graphite felt electrodes was also installed to generate electricity in the paddy field. The highest rice yield (9.0 ton/ha), dry mass (12.4 ton/ha), and protein content (13.1%), an important nutrient in animal feed, were obtained when a bottom-to-top irrigation (TWW was supplied to the underdrain pipe) was applied at the highest flow rate. The bottom-to-top irrigation achieved 79 to 91% removal of nitrogen in TWW, which was much higher than the top-to-top irrigation (58%). No accumulation of heavy metals was found in the experimental soils, and heavy metal concentrations in brown rice were lower than the allowable levels of current standards. The electric output from the MFC system was much lower than that reported in normal paddy fields, probably due to the poor connection between cables and electrodes. Further study is necessary to improve the electricity generation and to continuously monitor heavy metals in brown rice and the soil.