Background: Inadequate acetabular component orientation is associated with postoperative impingement, dislocation, and accelerated polyethylene wear. Computed tomography (CT)-based navigation systems provide accuracy for total hip arthroplasty (THA) but are not available in all facilities. Accelerometer-based navigation systems are inexpensive, but their accuracy remains undetermined. This study compares the accuracy of cup orientation in THA using CT-based and accelerometer-based navigation systems. Methods: This retrospective study included 35 consecutive patients (11 males, 24 females; mean age, 65 years) who underwent primary cementless THA via an anterolateral approach in the supine position. Both CT-based and accelerometer-based navigation systems were used simultaneously. The accuracy of cup orientation was compared between the two systems using postoperative CT. Results: The accuracy of cup inclination was 2.7°± 2.0°in the CT-based group and 3.3°± 2.4°in the accelerometer-based group. The accuracy of cup anteversion was 2.8°± 2.6°in the CT-based group and 3.4°± 2.2°in the accelerometer-based group. No significant difference was observed in cup inclination (p = 0.29) or cup anteversion (p = 0.34) between CT-based and accelerometer-based navigation. Conclusions: The accuracy of cup positioning did not differ significantly between CT-based and accelerometer-based navigation systems.