Noncoding RNAs (ncRNAs) regulate gene expression through RNA-chromatin interactions, yet their role in human brain evolution remains unclear. To map these interactions, we integrated FANTOM6 neurogenic data with a comprehensive atlas of regulatory regions active during early cortical development. This integration effort linked ncRNAs and transcription factors (TFs) to their genomic targets, revealing functional interactions captured by RNA-DNA contact mapping, yet largely missed by chromatin conformation data. Overlaying these interactions with nearly fixed variants in Homo sapiens relative to extinct hominins uncovered widespread rewiring of TF binding, affecting genes implicated in progenitor proliferation and neuronal differentiation. Gene regulatory network reconstruction identified TEAD2 and ONECUT2 as key regulators of intermediate progenitors and migrating neurons. Functional perturbation followed by Cut&Tag and ATAC-seq linked the two TFs to disease - and evolutionarily- relevant pathways. Together, these results show how ncRNA-TF cooperation and selective cis-regulatory rewiring contributed to sapiens-specific features of cortical development. ### Competing Interest Statement The authors have declared no competing interest. Spanish Ministry of Science, PID2023-146627NB-I00 AGAUR/Generalitat de Catalunya, 2021-SGR-313 Telethon Research Grant, GGP19226 RE-MEND, 101057604

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