ZIC2 is a transcription factor that, when mutated in humans, causes holoprosencephaly type 5 (HPE5) and other neurodevelopmental disorders. However, the molecular mechanisms by which ZIC2 deficiency leads to this kind of pathologies remain unclear. Here we first demonstrate that Zic2 is expressed transiently in cells of the three germ layers of the epiblast, as well as in the premigratory neural crest cells (NCCs) in mice. Then, by analysing Zic2 occupancy profiles during gastrulation and neurulation stages and the transcriptome of Zic2 mutant embryos, we observe that this transcription factor majorly binds to sequences near or in the TSS in both epiblast and NCCs. These analyses also define the gene program directly regulated by Zic2 in NCCs, including a highly significant number of genes involved in the epithelial-to-mesenchymal transition (EMT) process that belong to the Wnt, cadherin or TGF-β pathways. By functional experiments in vivo we then demonstrate that Zic2 blocks the Wnt pathway in premigratory NCCs at the time that activates the TGF-β signalling pathway to facilitate their delamination. Altogether these results reveal the importance of EMT deregulation in the etiology of Zic2-associated pathologies and may help to improve the diagnosis and genetic counseling of these conditions.