This study presents a workflow to predict the upscaled absolute permeability of the rock core direct from CT images whose resolution are not sufficient to allow direct pore-scale permeability computation. This workflow exploits the deep learning technique with the data of raw CT images of rocks and their corresponding permeability value obtained by performing flow simulation on high resolution CT images. The permeability map of a much larger region in the rock core is predicted by the trained neural network. Finally, the upscaled permeability of the entire rock core is calculated by the Darcy flow solver, and the results showed a good agreement with the experiment data. This proposed deep-learning based upscaling method allows estimating the permeability of large-scale core samples while preserving the effects of fine-scale pore structure variations due to the local heterogeneity.