Survival rates for total shoulder arthroplasty are critically dependent on the correct placement of the glenoid component. Especially in osteoarthritis, pathological version of the glenoid occurs frequently and has to be corrected surgically by eccentric reaming of the glenoid brim. The aim of our study was to evaluate whether eccentric reaming of the glenoid can be achieved more accurately by a novel computer assisted technique. Procedures were conducted on 10 paired human cadaveric specimens presenting glenoids with neutral version. To identify the correction potential of the navigated technique compared to the standard procedure, asymmetric reaming of the glenoid to create a version of -10° was defined as the target. In the navigated group, asymmetric reaming was guided by a 3D fluoroscopic technique. Postoperative 3D scans revealed greater accuracy for the eccentric reaming procedure in the navigated group compared to the freehand group, resulting in glenoid version of -9.8 ± 3.8° and -5.1 ± 4.1°, respectively (p < 0.05). Furthermore, deviation from preoperative planning was significantly reduced in the navigated group. These data indicate that our navigated procedure offers an excellent tool for supporting glenoid replacement in TSA.