The aim of this study is to investigate the accuracies and the agreements of the 3D Endo software, conventional CBCT software Romexis Viewer at three voxel sizes, and the EAL ProPex Pixi in endodontic length measurements. Three hundred and twenty-nine root canals in 120 intact human extracted molars were accessed. The actual lengths (AL) and electronic lengths (EL) were measured using the ruler and electronic apex locator (EAL), respectively. Teeth were scanned using the CBCT at different voxel sizes (0.075, 0.10, and 0.15 mm). Root canal lengths were measured using 3D Endo with proposed length (3D-PL) by software, corrected length (3D-CL), Romexis Viewer. The Fisher’s exact test, paired t-test and Bland–Altman plots were calculated to detect the agreements of the four methods with AL measurements. The ProPex Pixi measurements obtained the highest accuracy in the range of ± 0.5 mm. There was agreement between the 3D-PL and the 3D-CL with AL measurements at voxel size of 0.15 mm and at voxel size of 0.10 mm, respectively. The CBCT Romexis Viewer measurements agreed with AL at three voxel sizes. The conventional CBCT measurements using Romexis Viewer and dedicated software did not reach to the 100% accuracy in the range of ± 0.5 mm.