The aim of this prospective clinical and magnetic resonance imaging study was to analyze the effect of 1-year Activator (Yi-fan Dental Co., Shanghai, China) treatment in internal anatomical relationships of the temporomandibular joint (TMJ) complex, including the condyle-disc relationship, condyle-fossa relationship, condylar height change, disc length change, and morphologic change of the glenoid fossa. The study was composed of patients with class II division 1 malocclusion (11 girls and 13 boys) who underwent 1-year Activator treatment. All the patients were in the acceleration or peak phase of the pubertal growth spurt. Magnetic resonance imaging in closed-mouth position and lateral cephalometric radiographs before and after 1 year of Activator treatment were analyzed metrically. Overall, condylar height showed a significant increase (P < 0.001), and the eminence angle decreased (P = 0.037). TMJ disc length has no statistically significant change before and after treatment. A slight advancement (P = 0.041) was found in the sagittal condylar position. A significant backward movement (P = 0.04) was shown in the sagittal disc position. Our results showed that the disc is not impaired by Activator therapy; it seems possible that adaptive remodeling, including a shallower glenoid fossa and increased condylar height, was seen after treatment.