A method and apparatus are provided for using a neural network to estimate scatter in X-ray projection images and then correct for the X-ray scatter. For example, the neural network is a three-dimensional convolutional neural network 3D-CNN to which are applied projection images, at a given view, for respective energy bins and/or material components. The projection images can be obtained by material decomposing spectral projection data, or by segmenting a reconstructed CT image into material-component images, which are then forward projected to generate energy-resolved material-component projections. The result generated by the 3D-CNN is an estimated scatter flux. To train the 3D-CNN, the target scatter flux in the training data can be simulated using a radiative transfer equation method.