Temperature profiles of the hot galaxy cluster intracluster medium (ICM) have a complex non-linear structure that traditional parametric modelling may fail to fully approximate. For this study, we made use of neural networks, for the first time, to construct a data-driven non-parametric model of ICM temperature profiles. A new deconvolution algorithm was then introduced to uncover the true (3D) temperature profiles from the observed projected (2D) temperature profiles. An auto-encoder-inspired neural network was first trained by learning a non-linear interpolatory scheme to build the underlying model of 3D temperature profiles in the radial range of [0.02-2] R500, using a sparse set of hydrodynamical simulations from the THREE HUNDRED PROJECT. A deconvolution algorithm using a learning-based regularisation scheme was then developed. The model was tested using high and low resolution input temperature profiles, such as those expected from simulations and observations, respectively. We find that the proposed deconvolution and deprojection algorithm is robust with respect to the quality of the data, the morphology of the cluster, and the deprojection scheme used. The algorithm can recover unbiased 3D radial temperature profiles with a precision of around 5% over most of the fitting range. We apply the method to the first sample of temperature profiles obtained with XMM-Newton for the CHEX-MATE project and compared it to parametric deprojection and deconvolution techniques. Our work sets the stage for future studies that focus on the deconvolution of the thermal profiles (temperature, density, pressure) of the ICM and the dark matter profiles in galaxy clusters, using deep learning techniques in conjunction with X-ray, Sunyaev Zel'Dovich (SZ) and optical datasets.