The main objective of this systematic review was to collect the pre-existing scales for assessing the difficulty of third molar extraction. The secondary objective was to design a proposal for a preoperative evaluation protocol for the difficulty of third molar extraction. Two independent researchers conducted an electronic search in Pubmed (MEDLINE), Cochrane, and Scopus databases during March 2021. Included studies evaluated the prediction of the difficulty of surgical removal of impacted upper or lower third molars using new indices/scales or pre-existing scales with or without modifications. Articles referring to coronectomies or assessing pre-surgical difficulty using other tools were excluded. Neither language nor publication date restrictions were applied. Out of 242 articles, 13 prospective cohort studies were finally selected. Seven developed new indices/scales, and 6 assessed the predictive ability of some pre-existing scales. Most of the indices/scales contained radiological variables and few added any patient-related variables. We proposed a preoperative assessment protocol of the difficulty of third molar extraction to facilitate treatment planning and/or considerate referral in cases of high difficulty. This proposal used patient-related, radiological and surgical variables. Using a preoperative protocol to evaluate the surgical difficulty, including different patient-specific, radiological and surgical variables, could facilitate treatment planning, help clinicians prevent complications and assess the possibility of referral.