Introduction: The aim of the study was to compare the changes in the skeletal and dentoalveolar structures in Malay patients with Class II Division 1 malocclusion treated by prefabricated re-mouldable customizable functional appliance (T4FTM) and Twin Block (TB) appliance. Methods: A randomised clinical trial was carried out with samples randomly assigned to active (TB appliance) and experimental (T4FTM appliance) groups. Pre- and post-treatment lateral cephalometric radiographs were taken for each subject and the overjet was clinically measured at the same intervals. 20 angular and linear measurements were chosen and measured separately. Results: Independent t test was used to compare the changes between the two groups. A significant difference between the groups was seen with overjet at 2.14 mm (p < 0.01), Sv_Pog distance at 1.83mm (p < 0.05), Sv_ii distance at 2.55 mm (p < 0.001), horizontal distance from the upper to the lower incisor tip at 1.81 mm which was statistically significant (p < 0.05). The other variables SNB and ANB angles too showed a significant difference. However, all the favourable changes were noted in the TB group. Conclusion: T4FTM appliance could be an effective appliance for the management of British Standard Institute's Class II Division 1 malocclusion on Class II skeletal pattern. However, the TB group differed significantly and had a more favourable correction in terms of the sagittal skeletal and dentoalveolar discrepancy.