Endodontic treatment consists of different working procedures, such as the isolation of the operating field, pulp chamber access, and cleaning and shaping phases with at last the need of a three-dimensional filling of the canals. Each step requires a series of single-use or sterilizable instruments. We have performed a systematic review of different sterilization and disinfection procedures aiming at drawing up a disinfection and sterilization procedure to be used on endodontic instruments. A search on PubMed and Scopus was carried out using the following keywords: “endodontic sterilization,” “endodontic autoclave,” “decontamination dental bur,” “sterilization dental burs,” and “gutta-percha points sterilization.” Eligible articles were included in the qualitative and quantitative analysis. Results of the meta-analysis showed that the most effective method in sterilization is autoclaving. The qualitative analysis showed that the use of single-use or first-use instruments requires presterilization or sterilization procedures, and for reusable tools, attention must be paid to the removal of debris deposited on the blades, not easy to remove manually.