© 2020, The Author(s). Herein, we introduce continuous sub-irrigation with treated municipal wastewater (TWW) as a novel cultivation system to promote resource recycling and cost-effective forage rice production in Japan. However, both TWW irrigation and forage rice cultivation were previously considered to intensify CH4 and N2O emissions. In the present study, therefore, we evaluate the emissions of greenhouse gases (GHGs) and yielding capacity of forage rice between conventional cultivation and continuous sub-irrigation systems employing different water supply rates. Results indicated that continuous sub-irrigation with TWW resulted in high rice yields (10.4–11 t ha−1) with superior protein content (11.3–12.8%) compared with conventional cultivation (8.6 t ha−1 and 9.2%, respectively). All TWW irrigation systems considerably reduced CH4 emissions, while higher continuous supply rates significantly increased N2O emissions compared with the conventional cultivation. Only the continuous irrigation regime employing suitable supply rates at appropriate timings to meet the N demand of rice plants decreased both CH4 and N2O emissions by 84% and 28%, respectively. Overall, continuous sub-irrigation with TWW provides high yields of protein-rich forage rice without the need for synthetic fertilisers and effectively mitigated GHG emissions from paddy fields.