Aim: The present clinical trial aimed to preliminarily assess whether navigation could help to position impacted supernumerary teeth (STs) and reduce surgical trauma. Materials and methods: Subjects with an impacted supernumerary tooth (ST) in the premaxillary area were enrolled in the study and randomly distributed into a navigation group and a control group. In the navigation group, STs were positioned and extracted under real-time optic navigation. In the control group, STs were extracted depending on the surgeon's experience. Subjects were followed up for 12 to 24 weeks postsurgery. Operating time, futile bony trauma, and the positioning precision of the STs were the major outcomes assessed. Multivariate correlation analysis was performed. Results: In 24 subjects, 32 STs were removed and no severe complications occurred in either group. The proportion of ST exposure at the planned access point was 100% in the navigation group and 68.75% in the control group (chi(2) = 5.926, P = 0.015). Futile length, futile width, and the distance between the point where the ST was initially exposed and the bony point planned for accessing it were related to both navigation/control grouping and bone thickness in the access side. For challenging STs with bone thickness of > 0.5 mm in the access side (N = 22), the futile length in the navigation group (0.0 [0.0, 4.0] mm) was significantly smaller than that in the control group (3.0 [0.0, 8.0] mm, P = 0.028). Similarly, the futile width in the navigation group (0.0 [0.0, 2.0] mm) was significantly smaller than that in the control group (2.0 [0.0, 4.0] mm, P = 0.018). Conclusions: Navigation helped to position impacted STs precisely and reduced surgical bony trauma to some extent, especially in challenging cases in which the bone in the access side was thicker than 0.5 mm.