Background/AimThis study aimed to develop a protocol that combines cone‐beam computed tomography (CBCT), software, and 3D printing to design 3D replicas for tooth autotransplantation. The goal was to evaluate the impact of this approach on the extraoral time of the donor teeth and the total surgical time, thereby enhancing surgical efficiency and outcomes.Materials and MethodsA non‐randomized trial (protocol 10.1186/ISRCTN13563091) was conducted at Riga Stradins University, enrolling 46 patients (13–22 years old) who required molar extraction and possessed a non‐erupted third molar. The patients were sequentially assigned to a 3D replica group (24 patients) or a control group (22 patients). The primary outcome measured was the extra‐alveolar time of the donor tooth, and the secondary outcome was the total duration of surgery. Both were assessed using a sample size capable of detecting a 10‐min difference. A generalized linear model adjusted for various factors was used to test for significant time differences (p < .05) between the groups.ResultsForty‐six patients were included in this analysis. The effect of using 3D replicas was not statistically significant and was associated with a decrease in the extraoral time of the donor tooth in seconds (β = −9.35, 95% CI [−40.86, 22.16]). For the total surgical time in minutes, the use of 3D replicas had a statistically significant impact, reducing the operation duration in minutes (β = −13.42, 95% CI [−24.50, −2.34]). No early complications were observed in either group, with all teeth present at 3–4 weeks post‐surgery.ConclusionsThe integration of 3D printing technology can enhance the efficiency of autotransplantation surgeries, primarily by reducing surgical time.