Black Vertosols of subtropical Australia emit large amounts of nitrous oxide (N2O) to the atmosphere under fertilizer-applied grain cropping compared to other Australian cropping soils. N2O emissions can be mitigated by either reducing fertilizer N inputs or altering crop rotation systems. In this study, the WNMM agroecosystem model was used to investigate the responses of N2O emissions from four different crop rotation systems including canola-wheat-barley (T1CaWB), chickpea-wheat-barley (T3CpWB), chickpea-wheat-chickpea (T4CpWCp), and chickpea-Sorghum (T5CpS) under projected future climate change scenarios on a black Vertosol at Tamworth, New South Wales, Australia. In simulations of the twenty-first century under four different scenarios for atmospheric greenhouse gas concentrations, the annual N2O emissions from the four cropping systems increased with greenhouse gas forcing of the climate. The annual N2O emissions from T4CpWCp (with no fertilizer N application) were the most sensitive to climate change, with 14.3–61.9% increase compared with historic simulations of 1952–2014. The simulated T5CpS treatment (with a long fallow) kept the gross margin-scaled N2O emissions below 1 g N per Australian dollar under all climate change scenarios. This suggests that the inclusion of a long fallow in a crop rotation system can slow down the pace of increasing gross margin-scaled N2O emissions in response to climate change. Our simulation results also imply that legume rotations as mitigation options on N2O emissions may not be resilient to the future changing climate even though they can greatly reduce N2O emissions under the current climate.