The purpose of this retrospective study was to first compare the clinical outcome of anatomical double-bundle (DB) anterior cruciate ligament reconstruction (ACLR) with hamstring tendon (HT) autografts and anatomical rectangular tunnel ACLR with bone-patellar tendon-bone (BPTB) autografts. Secondly, we aimed to demonstrate the quantitative locations of the femoral and tibial tunnel apertures using postoperative three-dimensional computed tomography (3D CT). Twenty-five patients underwent anatomical rectangular tunnel ACLR using BPTB grafts (Group B) and 23 patients underwent anatomical DB ACLR using HT grafts (Group H). All patients underwent subjective postoperative evaluations using the Lysholm score and Knee Injury and Osteoarthritis Outcome Score. Patients also underwent objective evaluations by the International Knee Documentation Committee score, the Lachman test, the pivot-shift test, and range of motion. In addition, we quantitatively assessed anterior knee stability using a KneeLax3 arthrometer and thigh strength. All evaluations except for thigh strength were assessed for a minimum 2 years of follow-up period. Femoral and tibial tunnel aperture locations were quantitatively evaluated postoperatively using 3D CT images in all patients. BPTB grafts showed significantly better anterior knee stability than HT grafts (0.1 mm versus 1.1 mm, p = 0.01), although there were no significant differences in other objective and all subjective evaluations between the two graft types. Morphometric analysis of femoral and tibial tunnel locations revealed that the two procedures were based on the same anatomical concept. In conclusion, BPTB grafts showed significantly better anterior knee stability than HT grafts, although no significant differences in other objective evaluations and all subjective evaluations were detected between the two graft types in anatomical ACLR. Additional 3D CT data validated the anatomical concepts of these two procedures.