Aim: The purpose of this study was to compare the residual dentin thickness after manual and rotary instrumentation technique in primary root canals using CBCT. The null hypothesis was that there is no difference in the cleaning efficiency of both manual and rotary technique. Methodology: Manual filing was performed on 30 root canals using stainless steel S-files. Rotary instrumentation was carried out on a further 30 root canals, using rotary ProTaper files in a 300-rotation per minute (r.p.m.) Handpiece (NSK Endomate DT) according to the manufacturer’s instructions. The roots were aligned perpendicularly to the beam, and they were scanned before and after instrumentation by using the CBCT operating at 60 kV and 2.5mA. Pre-instrumentation and post-instrumentation measurements of canals were performed by using the Carestream 3D software. Results: When both the manual and rotary methods of canal instrumentation were compared, it was found that the reduction of dentinal thickness with respect to the manual method was more than the rotary method. Conclusions: There was more dentine thickness reduction in manual instrumentation than rotary instrumentation for root canal preparation in primary teeth.