This study aimed to evaluate the soft-tissue changes in the long-term after miniscrew-assisted rapid palatal expansion (MARPE) and conventional rapid palatal expansion (RPE) appliances compared with a matched control group using voxel-based superimposition of cone-beam computed tomography (CBCT) scans. A total of 180 CBCTs for 60 patients at 3-time points were evaluated: pretreatment (T1), postexpansion (T2), and posttreatment (T3) for 3 groups: (1) MARPE, (2) RPE, and (3) controls (time-period T1 to T3: MARPE, 2 years 8 months; RPE, 2 years 9 months; control, 2 years 7 months). The voxel-based superimposition technique was used to superimpose the CBCT scans, after which the soft-tissue surfaces were extracted from the superimposed T1-CBCT, T2-CBCT, and T3-CBCT scans. Nine landmarks were identified on the CBCT scans: nasion, A-point, pogonion, right and left alar base, right and left zygoma, and right and left gonion. The coordinates of the 9 parameters were obtained in the x-axis, y-axis, and z-axis for the CBCT scans and subjected to statistical analyses. The changes in the soft-tissue surfaces were also evaluated by color-coded maps for short-term (T2) and long-term (T3) changes. The mean changes from T1 to T2 and T1 to T3 were tested against no change within the groups by paired t test, and the mean changes among the 3 groups were compared with analysis of variance F test with Tukey's Honest significant difference used for adjusting P values for multiple testing. In the short term, both MARPE and RPE led to a significant downward movement of pogonion, left gonion, and lateral movement of the right and left alar base compared with controls at T2 (P<0.05). In addition, MARPE led to a significant downward movement of right gonion than controls at T2 (P<0.05). Moreover, RPE led to a significant downward and forward movement of A-point and downward movement of the right and left alar base than controls at T2 (P<0.05). However, in the long-term, there were no significant differences in the soft-tissue changes among the MARPE, RPE, and control groups. MARPE and RPE do not lead to significant soft-tissue changes in the long term when compared with controls.