Traumatic dental injuries of permanent teeth result in multiple immediate and long-term consequences depending upon the severity of trauma, age of the patient, the status of root maturity, and the emergency care provided. The healing responses may get disturbed due to severe damage, loss of vascularity of the supporting structures, and infections. As a result, the prohealing mediators and pathways are overpowered by the destructive stimuli often manifested by an increased osteoclastic activity. Among the various late complications, the apical periodontitis or the periapical lesions are most worrisome for the patients and create clinical dilemma for the dentists. In the past, many such lesions were classified as cysts and subjected to surgical management. However, better understanding of lesion pathophysiology, three-dimensional imaging, and molecular pathways have established their inflammatory nature. The advancements in materials such as calcium silicates, and regenerative techniques have propelled the research related to non-surgical endodontic management as its clinical acceptability. The treatment largely follows the recommendations of regenerative medicine and is based on four principles: (a) establishing the drainage or an endodontic access to the area, (b) removal of most of the triggering agents such as necrosed pulp, toxins, and inflammatory mediators, (c) disinfection of the area, controlling inflammation and reversal of the acidic pH, and (d) maintenance of this infection/inflammation-free state for a long time through adequate sealing. This review aims to highlight the rationale of the approach, case selection, pathophysiology of the causation and healing, clinical protocols, and the limitations of non-surgical endodontic management of large periapical lesions secondary to traumatic dental injuries.