Apical extrusion of debris during endodontic treatment is considered one of the main causes of postoperative pain and inflammation and is influenced by the instrumentation system used. Technological advances, particularly the development of nickel-titanium (NiTi) alloys and rotary systems such as ProTaper® Universal and ProTaper® Ultimate, have provided greater flexibility, reduced clinical time, and decreased debris extrusion. However, uncertainties remain regarding the impact of these different systems on patients’ perception of postoperative pain. This randomized clinical study aims to evaluate postoperative pain in posterior teeth undergoing endodontic treatment using these two instrumentation systems. A total of 124 patients aged between 19 and 92 years will be randomly assigned to two groups (PU and PTU). Root canal preparation will be performed according to the manufacturers’ recommended protocols, with standardized irrigation procedures and single-use instruments. Postoperative pain will be assessed using the Visual Analog Scale (VAS) at 24 hours, 48 hours, 72 hours, and 7 days after treatment. The study will follow ethical guidelines, including informed consent and participant confidentiality. Statistical analyses will be conducted to compare pain intensity between groups while considering variables such as age, sex, and the need for analgesic medication. The expected findings may help determine which instrumentation system is more closely associated with improved postoperative comfort, providing evidence to support a more predictable, safer, and less painful endodontic practice for patients.