© Author(s) 2016. The clearing and burning of tropical savanna leads to globally significant emissions of greenhouse gases (GHGs); however there is large uncertainty relating to the magnitude of this flux. Australia's tropical savannas occupy the northern quarter of the continent, a region of increasing interest for further exploitation of land and water resources. Land use decisions across this vast biome have the potential to influence the national greenhouse gas budget. To better quantify emissions from savanna deforestation and investigate the impact of deforestation on national GHG emissions, we undertook a paired site measurement campaign where emissions were quantified from two tropical savanna woodland sites; one that was deforested and prepared for agricultural land use and a second analogue site that remained uncleared for the duration of a 22-month campaign. At both sites, net ecosystem exchange of CO2 was measured using the eddy covariance method. Observations at the deforested site were continuous before, during and after the clearing event, providing high-resolution data that tracked CO2 emissions through nine phases of land use change. At the deforested site, post-clearing debris was allowed to cure for 6 months and was subsequently burnt, followed by extensive soil preparation for cropping. During the debris burning, fluxes of CO2 as measured by the eddy covariance tower were excluded. For this phase, emissions were estimated by quantifying on-site biomass prior to deforestation and applying savanna-specific emission factors to estimate a fire-derived GHG emission that included both CO2 and non-CO2 gases. The total fuel mass that was consumed during the debris burning was 40.9 Mg C ha-1 and included above- and below-ground woody biomass, course woody debris, twigs, leaf litter and C4 grass fuels. Emissions from the burning were added to the net CO2 fluxes as measured by the eddy covariance tower for other post-deforestation phases to provide a total GHG emission from this land use change. The total emission from this savanna woodland was 148.3 Mg CO2-e ha-1 with the debris burning responsible for 121.9 Mg CO2-e ha-1 or 82 % of the total emission. The remaining emission was attributed to CO2 efflux from soil disturbance during site preparation for agriculture (10 % of the total emission) and decay of debris during the curing period prior to burning (8 %). Over the same period, fluxes at the uncleared savanna woodland site were measured using a second flux tower and over the 22-month observation period, cumulative net ecosystem exchange (NEE) was a net carbon sink of -2.1 Mg C ha-1, or -7.7 Mg CO2-e ha-1. Estimated emissions for this savanna type were then extrapolated to a regional-scale to (1) provide estimates of the magnitude of GHG emissions from any future deforestation and (2) compare them with GHG emissions from prescribed savanna burning that occurs across the northern Australian savanna every year. Emissions from current rate of annual savanna deforestation across northern Australia was double that of reported (non-CO2 only) savanna burning. However, if the total GHG emission, CO2 plus non-CO2 emissions, is accounted for, burning emissions are an order of magnitude larger than that arising from savanna deforestation. We examined a scenario of expanded land use that required additional deforestation of savanna woodlands over and above current rates. This analysis suggested that significant expansion of deforestation area across the northern savanna woodlands could add an additional 3 % to Australia's national GHG account for the duration of the land use change. This bottom-up study provides data that can reduce uncertainty associated with land use change for this extensive tropical ecosystem and provide an assessment of the relative magnitude of GHG emissions from savanna burning and deforestation. Such knowledge can contribute to informing land use decision making processes associated with land and water resource development.