The aim of this study is to provide a novel method to perform Enlow’s neutral track analysis on cone-beam computed tomography (CBCT) images. Eighteen CBCT images of skeletal Class I (ANB = 2° ± 2°) subjects (12 males and 6 females, aged from 9 to 19 years) with no history of previous orthodontic treatment were selected. For each subject, 2D Enlow’s neutral track analysis was performed on lateral cephalograms extracted from CBCT images and 3D neutral track analysis was performed on CBCT images. A Student’s t-test did not show any statistically significant difference between the 2D and 3D measurements and therefore the method proposed by this study to realize the neutral track analysis on 3D images is valid and superimposable on that described by Enlow on lateral cephalograms. Further studies with a large sample and different skeletal class subjects are needed to confirm the results of this research.