Neuroimaging has entered the era of big data. However, the advancement of preprocessing pipelines falls behind the rapid expansion of data volume, causing substantial computational challenges. Here we present DeepPrep, a pipeline empowered by deep learning and a workflow manager. Evaluated on over 55,000 scans, DeepPrep demonstrates tenfold acceleration, scalability and robustness compared to the state-of-the-art pipeline, thereby meeting the scalability requirements of neuroimaging.