Suitable nitrogen (N) fertilisation is key for economic and environmental sustainability of croplands, and little is known on the potential of slow-release N sources to mitigate nitrous oxide (N2O) and methane (CH4) emissions in paddy rice growing in subtropical lowlands. We assessed the impact of controlled-released N fertiliser (CRNF) on partial global warming potential (pGWP) and yield-scaled greenhouse gas (GHG) emissions (GHG emission per unit of yield) in comparison to common urea in irrigated rice growing in a Typic Albaqualf in southern Brazil. The field experiment comprised four treatments: (1) control; (2) common urea applied into three splits, and CRNF applied at rice sowing; (3) on soil surface; and (4) in the seeding furrow. The N fertilisers did not increase N2O emissions when compared to control with exception of CRNF at the seeding furrow. However, N fertilisation increased CH4 emissions, with exception of the CRNF applied to the seeding furrow. Rice grain yields (7954–8637 kg ha−1) were not affected by N sources. The pGWP (11 683–14 297 kg CO2 eq ha−1) and the yield-scaled GHG (1.47–1.74 kg CO2 eq kg−1 grain) were similar among N sources. N fertilisation is a crucial practice to obtain high rice yields, which did not affect negatively the yield-scaled GHG emissions in this subtropical environment under continuous flood irrigation. CRNF applied at rice sowing provides rice grain productivity and agronomic efficiency similar to common urea applied into three splits.