Poised enhancers marked by H3K27me3 in pluripotent stem cells have been implicated in the establishment of somatic expression programs during embryonic stem cell (ESC) differentiation. However, the functional relevance and mechanism of action of poised enhancers remain unknown. Using CRISPR/Cas9 technology to engineer precise genetic deletions, we demonstrate that poised enhancers are necessary for the induction of major anterior neural regulators. Interestingly, circularized chromosome conformation capture sequencing (4C-seq) shows that poised enhancers already establish physical interactions with their target genes in ESCs in a polycomb repressive complex 2 (PRC2)-dependent manner. Loss of PRC2 does not activate poised enhancers or induce their putative target genes in undifferentiated ESCs; however, loss of PRC2 in differentiating ESCs severely and specifically compromises the induction of major anterior neural genes representing poised enhancer targets. Overall, our work illuminates an unexpected function for polycomb proteins in facilitating neural induction by endowing major anterior neural loci with a permissive regulatory topology. Display omitted •Poised enhancers are necessary for the induction of major anterior neural genes•Poised enhancers physically contact their target genes in embryonic stem cells•The interaction between poised enhancers and their target genes is PRC2 dependent•PRC2 provides major anterior neural loci with a permissive regulatory topology Cruz-Molina et al. demonstrate that pluripotent-associated poised enhancers are necessary for the induction of anterior neural genes. Poised enhancers physically interact with their target genes in embryonic stem cells in a PRC2-dependent manner. Thus, polycomb proteins might facilitate neural induction by providing anterior neural loci with a permissive regulatory topology.