This study aimed to explore the effects of biochar on pulse CO2 and N2O emissions and N cycling microbial functional genes after a short-term drought through a soil incubation experiment. Soil samples were collected in a macadamia orchard where biochar was applied 5 years prior to the incubation. Samples were wetted after being subjected to short-term (2-month) drought conditions. Samples were analysed for gas emissions (N2O and CO2), available NH4+-N, and NO3−-N, water soluble organic carbon (WSOC), water soluble total N (WSTN), and N cycling microbial gene abundance for a period of 21 days post-drought. Soil CO2 emissions were significantly higher in the drought-affected soil with no biochar than in the control soil with no biochar. No effect of biochar was detected on CO2 emissions for drought-affected soil. Available labile C (WSOC) in drought-affected soil was higher than in soils not subjected to drought, regardless of the presence of biochar. Therefore, C loss after adding water could be explained by the release of labile C accumulated during drought. Drought-affected soil with biochar did not influence N2O emissions compared with control soil subject to drought. In soils not subjected to drought, biochar had higher NO3−-N than the soil without biochar at day 7 post-drought, which could partly be explained by increased soil ammonia-oxidising bacteria (AOB) gene abundance. Our study suggested that a pulse C loss was more likely to occur post-drought whereas pulse N loss through N2O emission was not evident regardless of biochar application particularly within first day after being rewetted. Our study highlights the pulse effects of drought on GHG emissions from the soil after being wetted.