Improved N fertilizer management practices can increase rice yields and mitigate global warming potential (GWP). While banding N has been shown to have positive effects on yield and nitrogen use efficiency (NUE), there is little information on how it affects greenhouse gas (GHG) emissions from flooded rice systems. We tested the hypothesis that in continuously flooded rice systems where GWP is dominated by CH4 emissions, deep placement of urea in bands would reduce CH4 and N2O emissions. Rice yields and GHG emissions were measured from three field experiments which had three treatments: (1) no N (N0), (2) urea broadcast (U-BR) on soil surface and (3) urea banded at 7.5 cm soil depth (U-BA). All urea was applied in a single application before flooding in preparation for planting at N rates of 143–150 kg N ha− 1. Throughout the rice growing season GHG emissions were measured using a vented flux chamber and gas chromatograph. Across all fields, N fertilizer application increased yield on average by 121%. Between the N placement methods, grain yields and NUE (37 kg grain kg− 1) were similar. Daily N2O emissions were low to negative and did not differ among treatments. CH4 emissions were the major source of GWP emissions and cumulative emissions ranged from 6.3 to 297 kg CH4–C ha− 1 season− 1 among fields. While in some cases fertilizer N increased CH4 emissions, there was no effect of N placement on them.