© 2021 The Author(s).Objectives: This controlled study aimed to evaluate the effects of Herbst therapy on the trabecular structure of the condyle and angulus mandible using fractal dimension analysis (FD-A) accompanied by skeletal cephalometric changes. Material and method: The panoramic and cephalometric radiographs of 30 patients with skeletal Class II malocclusion treated with the Herbst appliance (C II-H group, mean age: 15.23 ± 1.08), 30 patients with skeletal Class II malocclusion that received fixed orthodontic treatment (C II-C group, mean age: 15.73 ± 1.38), and 30 patients with skeletal Class I malocclusion (C I-C group, mean age: 15.90 ± 1.30) were selected. FD-A was performed on the superoposterior region (C-SP) and centre of the condyles (C-C) and the mandibular angulus (Ang) on the panoramic radiographs taken at the pretreatment (T0), intermediate stage of treatment (T1), and posttreatment (T2) timepoints just like cephalometric analysis. Results: Herbst therapy provided a statistically significant increase in SNB, ANS-Me, Na-Me, S-Go, Co-Gn and a decrease in ANB and overjet (P < 0.05). All skeletal changes remained stable during the fixed appliance treatment after Herbst. The FD values in C-C increased (P < 0.05), and C-SP values decreased (P < 0.05) during Herbst therapy, while after removal of the Herbst appliance, no significant change was observed despite an increase in C-SP. The Ang value did not change during Herbst treatment, but then increased significantly (P < 0.05). There was no significant change in the FD values of the C I-C and C II-C groups at any stage of treatment. The C-C and C-SP changes at T1-T0 period, C-SP and Ang changes at T2-T1 period, and C-C, C-SP, and Ang values at T2-T0 period were found higher in C II-H group compared with the C II-C group significantly (P < 0.05). Conclusion: Herbst therapy changed the trabecular structure of the condyles in different directions at the superoposterior and central regions of the condyles, while the structural complexity of the angulus mandible, which did not change during the Herbst treatment, increased during the fixed orthodontic treatment after Herbst.