Purpose: This study aimed to compare the pediatric nickel-titanium (Ni-Ti) rotary system and manual instrumentation for root canal preparation for primary molar teeth to assess their efficiency in preparation time and cleaning capacity. Material and methods: Sixty-four primary molar canals were categorized into two groups randomly—Group I, 27 canals manually instrumented with K-files; and group II, 31 canals instrumented with Ni-Ti rotary files (Kedo-SG). India ink was injected into the root canals in both groups with insulin syringes. The instrumentation times were recorded; thereafter, the teeth were cleared using various solutions, following which, two observers evaluated and observed the root canals under a stereomicroscope. Results: The preparation time in group I using K-files was significantly longer than that in group II, which used exclusive pediatric primary tooth rotary files (group I vs. group II, 01:30 vs. 00:58, respectively; P=.0202; t-test, P<.001). Moreover, the rotary files demonstrated significant canal cleaning capacity than the K-files for complete cleaning of the root canals (approximately 38% vs. 8%, respectively; P=.013). Conclusion: The use of rotary files for preparation of primary molar teeth has several advantages over the manual K-files, including faster working time. Therefore, the use of rotary files will improve compliance with children, and additionally, provide acceptable cleaning capacity.