A method and system for automated correction of phase error in MRI-based flow evaluation employs a computer processor programmed to execute a trained convolutional neural network (CNN) to receive and process image data comprising flow velocity data in three directions and magnitude data collected from a region of interest over a scan period from magnetic resonance imaging instrumentation. The image data is processed using the trained CNN to generate three output channels with pixelwise inferred corrections for the flow velocity data which are further smoothed using a regression algorithm. The smoothed corrections are added to the original image data to generate corrected flow data, which may be used for flow visualization and quantization.