Background <p>Ni-Ti instruments with varying design features may lead to different levels of postoperative pain, which is a significant clinical concern, particularly in previously asymptomatic teeth. Therefore, the purpose of this randomized clinical trial is to compare postoperative pain following instrumentation with TruNatomy versus ProTaper Next Ni-Ti systems in mandibular molars with asymptomatic apical periodontitis.</p> Methods <p>90 healthy participants were randomly assigned to two groups: TruNatomy (TN) or ProTaper Next (PTN) instruments. After single-visit root canal treatments, participants were asked to rate their postoperative pain levels at 6, 12, 24, 48, and 72&#xa0;h and seven days later, using the Numerical Rating Scale (NRS) through an online questionnaire. In cases of pain, 400&#xa0;mg of ibuprofen was prescribed. Data from 80 participants were finally included in the analysis. Data were analyzed using the Mann-Whitney U, Friedman, and Fisher’s Chi-Square tests (<i>p</i> &lt; 0.05).</p> Results <p>There was no statistically significant difference in postoperative pain intensity at 6, 12, 24, and 48&#xa0;h and seven days between the groups (<i>p</i> &gt; 0.05). At the 72-hour time point, TN group showed statistically higher postoperative pain intensity (<i>p</i> &lt; 0.05). No statistically significant differences in the incidence of postoperative pain were observed at any of the time points (<i>p</i> &gt; 0.05). Analgesic intake and flare-up incidence were not significantly different between the groups (<i>p</i> &gt; 0.05).</p> Conclusion <p>Postoperative pain levels were not significantly influenced by the type of rotary Ni-Ti instrument. Both TN and PTN instruments led to low-level and similar postoperative pain intensity, minimal analgesic use, and a low incidence of flare-ups in teeth with asymptomatic apical periodontitis.</p> Trial registration <p>ClinicalTrials.gov ID NCT06545773, Registration Date 8 August 2024 (retrospectively registered).</p>