Objectives: The primary objective of the present study was to find the gold-standard accuracy of voxel-based superimposition of cone-beam computed tomography (CBCT) datasets with a protocol developed for the Dolphin Imaging 3D software. The secondary objectives were to analyze reproducibility and efficiency of this protocol. Study Design: Twenty-five CBCT datasets of patients with dental implants present were selected. Each Base Volume dataset was duplicated to create a second volume. Subsequently, both volumes were superimposed with a voxel-based protocol consisting of 3 successive steps “Side-by-side Superimposition”; “Overlay Superimposition”; and “Export Orientation to 2nd Volume”. The protocol's accuracy was evaluated by measuring the mean distance between the apex of each dental implant on the Base Volume and second volume datasets. Efficiency was given by the mean time needed to complete all superimposition steps. Reproducibility was analyzed by calculating the intraclass correlation coefficients. Results: Mean time needed to complete the protocol was 198 seconds. The protocol had a rotational accuracy of 0.10° to 019° and a translational accuracy of 0.20 to 0.24 mm. Intra-observer and inter-observer reproducibility were 1 and 0.921 to 1, respectively. Conclusions: The protocol is accurate, precise, reproducible, and efficient. The validation of this method enables unbiased analysis of surgical outcomes based on a single, user-friendly software product that is widely available in academic and clinical settings.