A flexible reamer system (FRS) for transportal anterior cruciate ligament reconstruction (ACLR) has been developed to overcome the technical challenges of a rigid reamer system. The purpose of this study was to investigate the safety and effectiveness of the two-portal technique using an FRS by evaluating femoral tunnel geometry. This study included 30 patients (mean age 30 ± 12.1) who underwent transportal single-bundle ACLR. Operations were performed with the two-portal technique using an FRS. Three-dimensional computed tomography was performed for all patients 2days after the operation. The femoral tunnel position, femoral graft bending angle, femoral tunnel length, and posterior wall breakage were evaluated. These radiologic outcomes were compared to previous literature-reported outcomes. The mean distances (measured as a percentage) from the posterior wall and the intercondylar notch roof to the femoral tunnel center were 29.6 ± 5.5% and 20.1 ± 6.7%, respectively. The femoral graft bending angle (108.4° ± 6.9°) was similar to that associated with the traditional transportal technique using a rigid reamer system, but it was less acute than that associated with the three-portal technique using an FRS. The femoral tunnel length (32.8 ± 4.5mm) was also similar to the results of the traditional transportal technique using a rigid reamer system, but it was shorter than that of three-portal technique using an FRS. The prevalence of posterior wall breakage was as low as the reported outcomes of the outside-in technique (2 cases, 6.6%). The two-portal technique for transportal ACLR using an FRS can achieve comparable femoral graft bending angle and femoral tunnel length compared with the conventional three-portal technique using the rigid reamer system and had a low risk of posterior wall breakage. Therefore, the two-portal technique using the FRS can be considered a safe and effective method for transportal ACLR. Retrospective case series; level of evidence, 4.