This study seeks to three-dimensionally assess soft tissue changes in the orofacial region following tooth-borne and bone-borne surgically assisted rapid maxillary expansion (SARME). This prospective cohort study included 40 skeletally mature patients with transverse maxillary hypoplasia. A tooth-borne distractor (Hyrax) was used for expansion in 25 patients. In the remaining 15, a bone-borne distractor (transpalatal distractor, TPD) was used. Cone beam computed tomography (CBCT) scans were acquired before treatment (T0) and 22 months later (T1). 3D models were constructed from CBCT data and superimposed using voxel-based matching. Distance maps between the superimposed 3D models were computed to evaluate the degree of skeletal and soft tissue changes in the maxillary region. Distance maps showed negative distances (mean -1.25 (±1.5) mm) in the middle of the upper lip, indicating posterior repositioning of this area. The cheek region showed positive changes (mean 1.66 (±1.1) mm), reflecting the underlying increase in maxillary width. There was no significant difference between the two groups in all measured distances (p > 0.05). Retro-positioning of the upper lip accompanied skeletal remodeling in the anterior alveolar region at a mean ratio of 88 %, while the cheek region followed 32 % of the alveolar expansion. Soft tissue changes following SARME include posterior repositioning of the upper lip and increased projection of the cheek area. These changes were comparable between bone-borne and tooth-borne appliances. This study provides clinicians with more information over the expected orofacial soft tissue changes following SARME.