Objectives The aim of this prospective study was to evaluate the short-term effects of full-time and night-time wear of functional appliances on the temporomandibular joint (TMJ) and masticatory muscles and to compare the differences in craniofacial structures, TMJ, and masticatory muscles with magnetic resonance imaging (MRI). Methods The study was carried out using cephalometric radiographs and MRI of 20 Class II patients who were treated with monoblock/twin-block appliances. The patients were divided into 2 groups: ten patients in Group 1 used their appliances all day, while ten patients in Group 2 were instructed to wear the appliances during sleep. After at least 6 months of uninterrupted treatment, post-treatment cephalograms and MRI were obtained for patients whose molar relationship improved by at least a half cusp width. Signal intensity ratios (SIR) of TMJ structures and morphological evaluations of masticatory muscles were done for all patients. Results It was found a significant increase in SIR values of the condylar process, articular disc, retrodiscal tissue, and masticatory muscles for all treatment groups. Length of the masseter and medial pterygoid muscles increased to varying degrees which left side of Group 2 was significantly increased (P < 0.05). The volume of all muscles also increased to varying degrees. Conclusions The cephalometric and MRI findings of this study show that the treatment effects were similar for both wear schedules.