(1) Background: Imageless computer navigation systems have the potential to improve the accuracy of acetabular cup position in total hip arthroplasty (THA). Popular imageless navigation methods include locating the patient in a three-dimensional space (registration method) while using a baseline to angle the acetabular cup (reference plane). This study aims to compare the accuracy of different methods for determining postoperative acetabular cup positioning in THA via the direct anterior approach. (2) Methods: Fifty-one participants were recruited. Optical and inertial sensor imageless navigation systems were used simultaneously with three combinations of registration methods and reference planes: the anterior pelvic plane (APP), the anterior superior iliac spine (ASIS) and the table tilt (TT) method. Postoperative acetabular cup position, inclination, and anteversion were assessed using CT scans. (3) Results: For inclination, the mean absolute error (MAE) was lower using the TT method (2.4° ± 1.7°) compared to the ASIS (2.8° ± 1.7°, p = 0.17) and APP method (3.7° ± 2.1°, p < 0.001). For anteversion, the MAE was significantly lower for the TT method (2.4° ± 1.8°) in contrast to the ASIS (3.9° ± 3.2°, p = 0.005) and APP method (9.1° ± 6.2°, p < 0.001). (4) Conclusion: A functional reference plane is superior to an anatomic reference plane to accurately measure intraoperative acetabular cup inclination and anteversion in THA using inertial imageless navigation systems.