Electrokinetic mining (EKM) is a novel method for rare earth element (REE) mining that can achieve green and efficient recovery of REEs. However, as yet, there is no accurate model for describing the electrokinetic transport of REEs in weathering crusts, and this hinders the wider application of EKM. The conventional model fails to capture the microscale transport physics occurring in the nanochannels that exist ubiquitously in weathering crusts. Consequently, the existing models cannot distinguish the mobilities of different REEs. Here, we report a new model for a more faithful description of the electrokinetic transport of REEs in weathering crusts that considers the ionic size, which has previously been neglected. We reveal that the electrokinetic transport of heavy REEs (HREEs) is faster than that of light REEs (LREEs) in weathering crusts, which is contrary to the predictions of conventional models. Our model was validated experimentally by measurements of the electrokinetic transport of two LREEs (La and Sm) and an HREE (Er) in weathering crusts. The speed of electrokinetic transport follows the order Er > Sm > La. Our findings suggest that the ionic size is a non-negligible factor affecting the electrokinetic transport of REEs in weathering crusts containing nanochannels. This work offers a constitutive model to describe the electrokinetic transport of REEs in weathering crusts, which promotes both theoretical developments and practical applications of EKM.