This study aimed to perform a three-dimensional assessment of the effects of Kinesio taping (KT) on mandibular condylar volume during Twin Block (TB) appliance therapy in individuals with skeletal Class II malocclusions. Thirty children (16 female, 14 male) aged between 10 and 15 years (12.80 ± 1.08) who were scheduled for TB therapy were randomly assigned to two groups of 15 patients each. One group (Group 1) received KT on the temporomandibular joint (TMJ) area with TB therapy while the other group (Group 2) only received the TB. KT was applied in cycles of 3 days, followed by 1 day off for 3 months. All patients underwent computed tomography (CT) scanning before KT and TB therapy (T0) and 3 months later (T1). Changes in right and left condylar volumes were measured (cm3) using a GE Advantage Workstation (General Electric Medical Systems, USA) and compared between the two groups using the Mann–Whitney U test and Wilcoxon signed-rank test. The KT group showed a significant differences in condylar volumes for both right (mean 0.13; p = 0.015; [0.04: 0.22]) and left condyle (0.30; p = 0.001; [0.18: 0.42]) from baseline (T0) to 3 months (T1). The comparisons between Group 1 and Group 2 revealed no statistically significant difference in initial and final condylar volumes for both the right (0.13; p > 0.05; [−0.16: 0.09]) and the left condyle (0.30; p > 0.05; [−0.04: 0.42]). Kinesio taping, which demonstrated a relative and slight increase on condylar volume, may provide clinical benefits such as a reduction in the duration of functional appliance use, decreased risk of relapse, and effective correction of overjet.