Background: Proper cleaning of root canals is crucial in endodontic treatments to prevent infections and ensure long-term success. Deciduous molars, having unique anatomical challenges, require precise techniques to remove debris effectively. Manual files, traditionally used, are compared to modern rotary systems like Kedo-S files, designed to enhance cleaning efficiency. This study aims to evaluate the efficacy of these tools using India ink-stained root canals in deciduous molars. Aim: The aim of this study was to compare the cleaning efficacy of manual and rotary endodontic files in deciduous molars, specifically their ability to remove India ink, used as an indicator of debris, from the root canals. Material and Method: Forty recently extracted deciduous molar teeth were selected, with their root canals stained with India ink. These teeth were randomly divided into two groups of 20: Group 1 was prepared using manual K files, and Group 2 with Kedo-S rotary files. Following instrumentation, each tooth was sectioned into coronal and apical parts, which were then examined under a stereomicroscope to assess cleaning efficacy by scoring the presence of residual India ink. Result: In the coronal sections, manual K files scored 8.2 ± 1.11 while Kedo-S rotary files scored 4.52 ± 1.23. In the middle sections, the scores were 9.35 ± 1.12 for manual K files and 5.96 ± 1.23 for Kedo-S rotary files. These results indicated that the Kedo-S rotary files demonstrated superior cleaning efficacy compared to the manual K files in both coronal and apical sections. Higher scores indicated more residual debris, and thus, the lower scores of Kedo-S rotary files highlighted their better performance in cleaning the root canals. Conclusion: The conclusion of this study was that Kedo-S rotary files are more effective than manual K files in cleaning the root canals of deciduous molars. This superior cleaning efficacy was statistically significant, as confirmed by the Student t-test and ANOVA, with a p-value of less than 0.05. This difference was particularly notable in the coronal and middle sections of the root canals, affirming the effectiveness of Kedo-S rotary files over manual K files in endodontic treatment.