Significance The neocortex is characterized by a six-layered structure that is critical to brain function. Cortical development requires proper generation and differentiation of neurons that migrate out from the ventricular zone to populate the cortex. This is regulated by Wnt/β-catenin signaling, which reduces gradually during cortical development. However, how the decreasing of Wnt/β-catenin signaling is regulated is largely unclear. We demonstrate that neddylation, a ubiquitylation-like protein posttranslational modification, targets β-catenin itself to inhibit Wnt/β-catenin signaling in the process. We also show that ablating Nae1, an obligative subunit of the E1 for neddylation, from cortical progenitor cells leads to similar phenotypes in β-catenin gain-of-function mice. This study reveals a previously unappreciated role of neddylation in regulating cortical lamination by targeting β-catenin signaling.