Background It has been demonstrated that using innovative root-end filling materials speeds up the success of Endodontic Microsurgery (EMS) on teeth having root filling but still suffering from posttreatment Apical Periodontitis (AP). However, this has reopened the discussion about the long-term effectiveness of EMS conducted on such teeth. Objectives This study aimsto assess the long-term clinical and radiographic outcomes of endodontic surgical procedures in molars with radiographic evidence of secondary AP. Methodology A literature review was undertaken utilizing different databases, including MEDLINE (through PubMed), EMBASE, and Web of Science. The terms used for the search were ‘endodontic microsurgery,’ ‘apical microsurgery,’ ‘periapical disorders,’ ‘root canal therapy,’ ‘apicoectomy,’ ‘retreatment,’ ‘treatment result,’ “retrograde obturation,” and ‘success rate.’ In order to choose the most reliable longitudinal data, specific inclusion and exclusion criteria were established in advance. Only studies that met inclusion criteria for clinical and radiographic outcomes were considered, including prospective clinical studies and randomized clinical trials with at least two-year follow-ups. Results The study of the databases yielded 561 articles in total. From the 115 articles with full texts available, unrelated articles (105) were removed. Our inclusion criteria were met by an overall of ten studies (six prospective clinical studies and four randomized clinical trials). With intervals for follow-up ranging from two to thirteen years, a pooled success rate of 91% from all 451 treated teeth included in the randomized clinical trials and a pooled success rate of 79% from a total of 839 encompassed teeth in the prospective clinical studies were observed. During the same length of time of observation, survival rates ranged from 78% to 100%. Smoking status, tooth position and type, the presence or absence of dentinal abnormalities, the thickness of the bone between the teeth (interproximal bone), and the substance used to fill the space at the end of the roots are the five predictive variables revealed. Conclusion When EMS is performed by skilled endodontists who can deliver high success rates and reliable results, teeth afflicted by secondary AP have a good prognosis and can be preserved.