This work aims to present an in-house low-cost computer-aided simulation (CASS) process that was recently implemented in the preoperative planning of complex osteotomies for limb deformities in children. Five patients admitted to the Unit of Paediatric Orthopaedics and Traumatology from April 2018 to December 2019, for correcting congenital or post-traumatic limb deformities were included in the study. Three-dimensional (3D) digital models were generated from Computed Tomography (CT) scans, using free open-source software, and the surgery was planned and simulated starting from the 3D digital model. 3D printed sterilizable models were fabricated using a low-cost 3D printer, and animations of the operation were generated with the aim to accurately explain the operation to parents. All procedures were successfully planned using our CASS method and the 3D printed models were used during the operation, improving the understanding of the severely abnormal bony anatomy. The surgery was precisely reproduced according to CASS and the deformities were successfully corrected in four cases, while in one case, the intraoperative intentional undersizing of the bone osteotomy produced an incomplete correction of a congenital forearm deformity. Our study describes the application of a safe, effective, user-friendly, and low-cost CASS process in paediatric orthopaedics (PO) surgery. We are convinced that our study will stimulate the widespread adoption of this technological innovation in routine clinical practice for the treatment of rare congenital and post-traumatic limb deformities during childhood.