The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9)(CRISPR/Cas9) technology is a new gene editing technique. Compared with the previous gene editing techniques, such as homing endonuclease technology, zinc finger nuclease technology and transcription activator-like effector nuclease technology, it has greater advantages in target specificity, operation simplicity, treatment completeness and broad applications. Hepatitis B, acquired immunodeficiency syndrome (AIDS), malaria and other infectious diseases have been the major problems in clinic. Scientists are trying to use CRISPR/Cas9 technology to solve these medical problems. This article mainly summarizes the progress on CRISPR/Cas9 technology applied in infectious diseases.