Fertilization with urea can lead to a loss of carbon dioxide (CO2) that was fixed during the industrial production process. The extent of atmospheric CO2 removal from urea manufacturing was estimated by the Industrial Processes and Product Use sector (IPPU sector). On its basis, the Intergovernmental Panel on Climate Change (IPCC) has proposed a value of 0.2 Mg C per Mg urea (available in 2006 revised IPCC guidelines for greenhouse gas inventories), which is the mass fractions of C in urea, as the CO2 emission coefficient from urea for the agricultural sector. Notably, due to the possibility of bicarbonate leaching to waters, all C in urea might not get released as CO2 to the atmosphere. Hence, in order to provide an accurate value of the CO2 emission coefficient from applied urea in the rice ecosystem, the CO2 emission factors were characterized under different levels of 13C-urea applied paddy field in the current study. The total CO2 fluxes and rice grain yields increased significantly with increasing urea application (110–130 kg N ha−1) and thereafter, decreased. However, with increasing 13C-urea application, a significant and proportional increase of the 13CO2C emissions from 13C-urea was also observed. From the relationships between urea application levels and 13CO2C fluxes from 13C-urea, the CO2C emission factor from urea was estimated to range between 0.0143 and 0.0156 Mg C per Mg urea. Thus, the CO2C emission factor of this study is less than that of the value proposed by IPCC. Therefore, for the first time, we propose to revise the current IPCC guideline value of CO2C emission factor from urea as 0.0143–0.0156 Mg C per Mg urea for Korean paddy soils.