The effect of elevated carbon dioxide (CO2) concentration on greenhouse gas (GHG) emission from semi-arid cropping systems is poorly understood. Closed static chambers were used to measure the fluxes of nitrous oxide (N2O), CO2 and methane (CH4) from a spring wheat (Triticum aestivum L. cv. Yitpi) crop-soil system at the Australian grains free-air carbon dioxide enrichment (AGFACE) facility at Horsham in southern Australia in 2009. The targeted atmospheric CO2 concentrations (hereafter CO2 concentration is abbreviated as [CO2]) were 390 (ambient) and 550 (elevated) mu mol/mol for both rainfed and supplementary irrigated treatments. Gas measurements were conducted at five key growth stages of wheat. Elevated [CO2] increased the emission of N2O and CO2 by 108 and 29%, respectively, with changes being greater during the wheat vegetative stage. Supplementary irrigation reduced N2O emission by 36%, suggesting that N2O was reduced to N-2 in the denitrification process. Irrigation increased CO2 flux by 26% at ambient [CO2] but not at elevated [CO2], and had no impact on CH4 flux. The present results suggest that under future atmospheric [CO2], agricultural GHG emissions at the vegetative stage may be higher and irrigation is likely to reduce the emissions from semi-arid cropping systems.