Background During non-surgical retreatment process, the products such as dentin debris, root canal fillings, irrigation solutions, microorganisms and remaining pulp tissues can extrude to the apical area and can cause the postoperative pain and flare-up. Thus, the aim of this study was to evaluatethe effect of EDDY and manual dynamic activation (MDA) techniques on postoperative pain (PP) associated with retreatment. Methods Ninety patients scheduled for retreatment were treated at a single visit. Non-vital mandibular premolar teeth diagnosed with asymptomatic apical periodontitis were included in this study. The patients were divided into two groups (n = 45) on the basis of the need for additional irrigation activation procedures (EDDY and MDA). The patients’ post-treatment pain levels were asked to rate the intensity of their pain on a 10-point numerical rating scale (NRS) at the 12th, 24th, 48th, and 72nd h and 7 days.The data were analyzed using the chi-square and Wilcoxon signed-rank test was used for within-group comparisons and Mann Whitney U test was used to compare the groups by time period. Results The difference in postoperative pain intensity between two groups was statistically significant at 12, 24, 48, and 72 h (p < 0.05). There was no significant difference at 7 days. Moreover, no statistically significant difference was found between the two groups in terms of gender and analgesic medication intake (p > 0.05). Pain intensity after the treatment was lesser in the MDA groupthanin the EDDY group at 12, 24, 48, and 72 h. Conclusion This study could lead us to conclude that the two activation systems can be used during endodontic retreatment with no difference at PP 7 days later. However, a comparison of the groups indicated that the EDDY resulted in significantly more PP at 12, 24, 48, and 72 h. Trial registration ClinicalTrials.gov Identifier: NCT04726670.