Infectious diseases make up an important threat to human health and there is an urgent need for new treatments to reduce morbidity and mortality caused by acute viral infections such as rhinovirus and dengue virus, and chronic viral infections such as human immunodeficiency virus-1 and hepatitis B virus. With the development of molecular biology technology, gene-editing technology targeting sequence-specific loci has become a powerful tool for the treatment of infectious diseases. Among them, the regular clustered regularly interspaced short palindromic repeats (CRISPR) -CRISPR associated protein 9 (Cas9) is widely used in cell lines and animal models because of its high efficiency, convenience and high specificity, which has become a promising model for the treatment of new infectious diseases. Currently, feasibility studies of the use of viral and non-viral vectors to deliver Cas9 into cells in the form of DNA, mRNA or protein and clinical trials assessing the in vivo applicability of CRISPR-Cas9 are under way. In this review, we outline the principles of CRISPR-Cas9, the latest research advances in the treatment of infectious diseases, the challenges and possible solutions to the technology, and look further into its future direction.