Currently, a significant number of drugs based on therapeutic nucleic acids are being under development for the treatment of oncological, inflammatory, infectious diseases, and metabolic disorders. A growing number of approved nucleic acid therapeutics demonstrate the potential of gene therapy approaches. Therapeutic nucleic acids realize their biological effect in the cytoplasm, while plasma membrane is the main barrier to their intracellular delivery. Therefore, specially designed carriers are often used during the development of such drugs. The optimal carrier should not only facilitate the internalization of nucleic acids, but also exhibit no toxic effects, provide stabilization, and must be suitable for large scale production at low cost. Cell penetrating peptides (CPPs) match all these requirements. CPPs are effective and low-toxic carriers of nucleic acids. They usually represent basic peptides with a positive charge at physiological pH that capable to form nanostructures with negatively charged nucleic acids. Numerous preclinical studies in which CPP has been used as a carrier have shown promising results. In some cases, CPP-containing drugs successfully passed through clinical trials and the implemented into clinical practice. In this review, we consider the variety of therapeutic nucleic acids and summarize the experience of using CPP for their intracellular delivery. In addition, the classification and mechanisms of CPP cellular uptake are discussed, the understanding of which will accelerate the development of new gene therapy drugs.