The vertical temperature profile in the atmosphere reflects a balance between radiative and convective processes and interactions with the oceanic and land surfaces. Changes in vertical temperature profiles can affect atmospheric stability, which in turn can impact various aspects of weather systems. In this study, we analyzed recent-past trends of temperature over the Australian region using a homogenized monthly upper-air temperature dataset and four reanalysis datasets (NCEP, ERA-Interim, JRA-55 and MERRA). We also used outputs of 12 historical and future regional climate model (RCM) simulations from the NSW/ACT (New South Wales/Australian Capital Territory) Regional Climate Modelling (NARCliM) project and 6 RCM simulations from the CORDEX (Coordinated Regional Downscaling Experiment) Australasian project to investigate projected changes in vertical temperature profiles. The results show that the currently observed positive trend in the troposphere and negative trend in the lower stratosphere will continue in the future with significant warming over the whole troposphere and largest over the middle to upper troposphere. The increasing temperatures are found to be latitude-dependent with clear seasonal variations, and a strong diurnal variation for the near surface layers and upper levels in tropical regions. Changes in the diurnal variability indicate that near surface layers will be less stable in the afternoon leading to conditions favoring convective systems and more stable in the early morning which is favorable for temperature inversions. The largest differences of future changes in temperature between the simulations are associated with the driving GCMs, suggesting that large-scale circulation plays a dominant role in regional atmospheric temperature change.