Purpose: This retrospective study aims to compare the accuracy of two different CAD/CAM systems in orthognathic surgery. The novelty of this work lies in the method of evaluating the accuracy, i.e., using an Iterative Closest Point (ICP) algorithm, which matches a pair of 2D or 3D point clouds with unknown dependencies of the transition from scan s_(k) to scan s_(k+1). Methods: The study population was composed of ten patients who presented to the Maxillofacial Surgery Department of the University “Sapienza” of Rome for the evaluation and management of skeletal malocclusions. The patients were divided into two groups, depending on the technique used: group 1: splintless group (custom-made cutting guide and plates); group 2: splint group (using a 3D-printed splint). STL files were imported into Geomagic^® Control X™ software, which allows for comparison and analysis using an ICP algorithm. The RMSE parameter (3D error) was used to calculate the accuracy. In addition, data were compared in two different patient subgroups. The first subgroup only underwent a monobloc Le Fort I osteotomy (p-value = 0.02), and the second subgroup underwent a Le Fort I osteotomy associated with a segmental osteotomy of the maxilla (p-value = 0.23). Results: Group 1 showed a 3D error of 1.22 mm ± SD 0.456, while group 2 showed a 3D error of 1.63 mm ± SD 0.303. These results have allowed us to compare the accuracy of the two CAD/CAM systems (p-value = 0.09). Conclusions: The ICP algorithm provided a reproducible method of comparison. The splintless method would seem more accurate (p-value = 0.02) in transferring the surgical programming into the operating room when only a Le Fort I osteotomy is to be performed.