Few studies have explored greenhouse gas (GHG) emissions from arable land in sub-Saharan Africa (SSA), and particularly from rice paddy fields, which can be a major source of methane (CH₄) and nitrous oxide (N₂O) emissions. This study examined the effect of drainage on CH₄ and N₂O emissions from rice fields in Rwanda under shallow drainage to 0.6 m, with the drain weir open four times per week, and deep drainage to 1.2 m with the weir open four times or two times per week. CH₄ and N₂O fluxes from the soil surface were measured on nine occasions during rice flowering and ripening, using a closed chamber method. Measured fluxes made only a minor contribution to total GHG emissions from rice fields. However, drainage depth had significant effects on CH₄ emissions, with shallow drainage treatment giving significantly higher emissions (~0.8 kg ha⁻¹ or ~26 kg CO₂-equivalents ha⁻¹) than deep drainage (0.0 kg) over the 44-day measurement period. No treatment effect was observed for N₂O fluxes, which ranged from low uptake to low release, and were generally not significantly different from zero, probably due to low nitrogen (N) availability in soil resulting from low N fertilization rate (in the region). Overall, the results suggest that deep drainage can mitigate CH₄ emissions compared with traditional shallow drainage, while not simultaneously increasing N₂O emissions.