Mechanisms are provided to implement an automated medical image processing pipeline selection (MIPPS) system. The MIPPS system receives medical image data associated with a patient electronic medical record and analyzes the medical image data to extract evidence data comprising characteristics of one or more medical images in the medical image data indicative of a medical image processing pipeline to select for processing the one or more medical images. The evidence data is provided to a machine learning model of the MIPPS system which selects a medical image processing pipeline based on a machine learning based analysis of the evidence data. The selected medical image processing pipeline processes the medical image data to generate a results output.