Mutations in the coding region of the FOXP2 transcriptor factor gene are known to cause speech and language impairment. Chromosomal rearrangements with breakpoints downstream the gene have been hypothesised to impair speech and cognitive abilities via physical separation of distant regulatory DNA elements. In this study, we used highly efficient targeted chromosomal deletions induced by the CRISPR/Cas9 genome editing tool to characterise two functional enhancers: FOXP2-Eproximal and FOXP2-Edistal, located in the intergenic region between FOXP2 and its adjacent MDFIC gene. FOXP2-Edistal, separated from FOXP2 by a chromosomal rearrangement in a case of speech and language impairment, was demonstrated to be functional in a luciferase assay. Deletion of any of these two functional enhancers in a neuroectodermal tumor cell-line downregulates FOXP2 and decreases FOXP2 protein levels, conversely it upregulates MDFIC and increases MDFIC protein levels. We expect these findings contribute to a deeper understanding of FOXP2 and MDFIC may pace the development of speech and language in the brain.