Congenital heart defects, facial dysmorphism and intellectual development disorder (CHDFIDD) is associated with mutations in CDK13 gene, which encodes a transcription regulating Cyclin-dependent kinase 13 (CDK13). Here, we focused on development of craniofacial structures and analyzed early embryonic stages of CHDFIDD mouse models with hypomorphic mutation in Cdk13 gene, which exhibits cleft lip/palate and knockout of Cdk13 with stronger phenotype including midfacial cleft. Cdk13 was found to be physiologically strongly expressed in the mouse embryonic craniofacial structures, namely in the forebrain, nasal epithelium and maxillary mesenchyme. We also uncovered that Cdk13-deficiency leads to development of hypoplastic branches of the trigeminal nerve including maxillary branch and additionally, we detected significant gene expression changes of molecules involved in neurogenesis (Ache, Dcx, Mef2c, Neurog1, Ntn1, Pou4f1) within the developing palatal shelves. These results, together with changes of gene expression of other key face-specific molecules (Fgf8, Foxd1, Msx1, Meis2 and Shh) at early stages in Cdk13 mutant embryos, demonstrate a key role of CDK13 in regulation of craniofacial morphogenesis.