Introduction: Pediatric rotary systems have the advantage of improved canal centricity and conservative canal preparation with better obturation quality. Pro AF Baby Gold and Pedoflex files are two exclusive pediatric rotary file systems that were introduced in recent times. Aim and objective: The aim of the present study is to compare and evaluate the dentine thickness, centering ability, canal transportation, and instrumentation time of Pro AF Baby Gold and Pedoflex files using cone beam computed tomography (CBCT). Materials and methods: A total of 40 extracted human primary molar teeth with a minimum 7 mm root length were included in the study and randomly divided into two groups: group I, Pro AF Baby Gold; group II, Pedoflex files. Teeth were imaged preoperatively with CBCT, then root canal preparation was done in both groups with respective files, followed by postoperative CBCT imaging to evaluate the dentin thickness, centering ability, and canal transportation of both groups. Instrumentation time was noted using a stopwatch. Results: There is a statistically significant difference in the instrumentation time; Pedoflex took a shorter time when compared to Pro AF Baby Gold files. Regarding canal transportation, there was no significant difference between the two files, with Pedoflex showing a better value than the other files. Regarding centering ability, there was no significant difference between the two files, with Pro AF Baby Gold having a better value than the other files (p < 0.001). Conclusion: From the findings of our present study, it was found that both systems were able to effectively shape curved root canals in terms of canal transportation and centering ability.