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Introduction: The success of root canal procedures depends on cleaning and shaping of canals. There are several instrumentation techniques available for root canal preparation. Recently, exclusive rotary file systems called Kedo-SG Blue and Prime-Pedo have been introduced for root canal preparation in primary teeth. The inherent flexibility of these files allows them to preserve the anatomy of curved canals in primary molars. Aim: To compare the instrumentation time, obturation time, and quality of obturation using two paediatric rotary file systems, Kedo-SG BlueTM and Prime-PedoTM, in mandibular primary molars. Materials and Methods: A randomised clinical trial was conducted in the outpatient Department of Paediatric and Preventive Dentistry, Narayana Dental College and Hospital, Nellore Andhra Pradesh, India, from February 1, 2019 to January 20, 2020. Fifty primary molars with necrotic pulp were included and randomly divided into two groups, with 25 teeth in each group. Group 1 and Group 2 were instrumented with Kedo-SG BlueTM and Prime-PedoTM, respectively. The time taken for instrumentation and obturation was noted in minutes, and the quality of root canal filling was recorded as optimal, underfilled, or overfilled. The data were statistically analysed using an independent Student's t-test for time measurements and a Chi-square test for the quality of obturation. Results: There was a statistically significant difference in instrumentation time and obturation time between the two groups (p-value=0.009; 0.011). The Kedo-SG BlueTM rotary system showed a better quality of obturation compared to the Prime-PedoTM rotary system, although the difference was not statistically significant (p-value=0.22). Conclusion: The Kedo-SG BlueTM rotary system demonstrated shorter instrumentation and obturation times, as well as a higher number of optimally filled canals compared to the Prime-PedoTM rotary system. Therefore, the Kedo-SG BlueTM rotary system exhibited better clinical performance in primary molars than the Prime-PedoTM rotary system. [ABSTRACT FROM AUTHOR]