To validate 3D methods for femoral version measurement, we asked: (1) Can a fully automated segmentation of the entire femur and 3D measurement of femoral version using a neck based method and a head‐shaft based method be performed? (2) How do automatic 3D‐based computed tomography (CT) measurements of femoral version compare to the most commonly used 2D‐based measurements utilizing four different landmarks? Retrospective study (May 2017 to June 2018) evaluating 45 symptomatic patients (57 hips, mean age 18.7 ± 5.1 years) undergoing pelvic and femoral CT. Femoral version was assessed using four previously described methods (Lee, Reikeras, Tomczak, and Murphy). Fully‐automated segmentation yielded 3D femur models used to measure femoral version via femoral neck‐ and head‐shaft approaches. Mean femoral version with 95% confidence intervals, and intraclass correlation coefficients were calculated, and Bland‐Altman analysis was performed. Automatic 3D segmentation was highly accurate, with mean dice coefficients of 0.98 ± 0.03 and 0.97 ± 0.02 for femur/pelvis, respectively. Mean difference between 3D head‐shaft‐ (27.4 ± 16.6°) and 3D neck methods (12.9 ± 13.7°) was 14.5 ± 10.7° (p < 0.001). The 3D neck method was closer to the proximal Lee (−2.4 ± 5.9°, −4.4 to 0.5°, p = 0.009) and Reikeras (2 ± 5.6°, 95% CI: 0.2 to 3.8°, p = 0.03) methods. The 3D head‐shaft method was closer to the distal Tomczak (−1.3 ± 7.5°, 95% CI: −3.8 to 1.1°, p = 0.57) and Murphy (1.5 ± 5.4°, −0.3 to 3.3°, p = 0.12) methods. Automatic 3D neck‐based‐/head‐shaft methods yielded femoral version angles comparable to the proximal/distal 2D‐based methods, when applying fully‐automated segmentations.