ObjectivesThe Functional Clear Aligner (FCA) is a novel orthodontic appliance designed for the treatment of Class II malocclusion with mandibular retrognathia in adolescents. The aim of this study was to investigate the biomechanical characteristics of the masticatory muscles, jawbone, and temporomandibular joint (TMJ) during mandibular advancement using either FCA or Class II elastics combined with clear aligner (Class II elastics) through finite element analysis.Materials and methodsA 3D finite element model of the ‘muscle-jawbone-TMJ-appliance’ system was constructed based on CBCT and MRI images of a boy with skeletal Class II malocclusion. Masticatory muscles included masseter, temporal, medial pterygoid, and lateral pterygoid muscles. The TMJ consists of the temporal bone’s glenoid fossa, disc, and mandibular condyle. To observe the biomechanical characteristics of the muscles and TMJ during orthodontic appliance wearing and the retention phase, two different protocols were used: Model 1: The mandibular advancement using FCA; Model 2: The mandibular advancement using Class II elastics.ResultsThe FCA group produced greater and more coordinated masticatory muscle forces compared to the Class II elastics group. Temporal and masseter muscles exhibited the most pronounced variation in muscle strength during mandibular advancement. The FCA group exhibited greater TMJ region stress compared to the Class II elastics group. Interestingly, the stress on the articular discs in both models decreased over time. Tensile stresses were observed in both the condyle and the posterior region of the articular fossa.ConclusionDuring skeletal Class II malocclusion treatment, masticatory muscle forces and stress on the TMJ were higher in the FCA group compared to the Class II elastics group. In both models, stress cushioning was provided by the articular disc.