Aim: To assess canal shape, dentin thickness, and risk of perforation after using rotary Fanta AF baby files versus manual Hedstrom (H) files in root canal instrumentation of extracted second primary molars. Materials and methods: Twenty-six extracted second primary molars were randomly assigned to two groups; in Group (I): Molars were instrumented by Rotary Fanta AF baby files while in Group (II): Molars were instrumented by Manual H-files. The amount of dentin removal, canal shape, and risk of perforation were evaluated by cone-beam computed tomography (CBCT) comparing the pre to post instrumentation images. Fracture resistance after instrumentation was assessed with a universal testing machine. Results: Regarding the overall comparison of the amount of dentin removal on the mesial and distal walls of the distal canal, a significant difference was present between Fanta AF baby files and H-files (P=0.013) and (P<0.001) respectively. Where H-files removed a higher amount of dentin with mean ±SD (0.10±0.04) and (0.13±0.05) than Fanta files (0.08±0.04) and (0.05±0.02). However, a non-significant difference was observed regarding the shaping ability (P=0.691), the incidence of risk of perforation (P=0.680), and the fracture resistance (P=0.189). Conclusion: The Fanta AF baby files seem to be more effective in preserving dentin thickness than H files, and it can be utilized as a better alternative in root canal instrumentation in primary molars.