Lip bumper (LB) therapy is used as a treatment approach for mild to moderate crowding without extraction of teeth. Previous studies demonstrated that LB increases arch length through molar uprighting and lateral expansion. However, the effects of LB on mandibular incisors are inconclusive. The controversial results from different studies may be due to limitations including absence of a control group and/or use of 2D radiography. To address this issue, the current retrospective longitudinal CBCT study compared a rapid maxillary expansion (RME) group with no lower treatment [16 patients (9 females, 7 males); median age 8.86 years at T1 and 11.82 years at T2] and an RME + LB group [18 patients (13 females, 5 males); median age 9.46 years at T1 and 12.10 years at T2]. The CBCTs taken before and after phase 1 treatment were 3D superimposed based on the mandibular structure and were measured to determine the angular and linear changes of the mandibular incisors over the course of LB treatment. For comparisons between different timepoints within a group, a Wilcoxon matched-pairs signed rank test was used. For intergroup comparisons, a Mann–Whitney U test was used. Both groups showed eruption and protrusion of the mandibular incisors during the observation period, while there was no significant change in proclination of the lower incisors. When comparing the discrepancy of change between groups, there was no statistically significant difference detected. In summary, by utilizing a longitudinal 3D database, the current study demonstrated that the effect of LB on the position of the mandibular incisors is limited.