To develop and validate a fully automated, deep-learning pipeline for measuring glenoid bone loss on 3D CT scans using linear-based, en-face view, and best-circle method. Shoulder CT scans of 81 patients were retrospectively collected between January 2013 and March 2023. Our algorithm consists of three main stages: (1) Segmentation, where we developed a U-Net to automatically segment the glenoid and humerus; (2) anatomical landmark detection, where a second network predicts glenoid rim points; and (3) geometric fitting, where we applied a principal component analysis (PCA), projection, and circle fitting to compute the percentage of bone loss. The performance of the pipeline was evaluated using DSC for segmentation and MAE and ICC for bone-loss measurement; intermediate outputs (rim point sets and en-face view) were also assessed. Automated measurements showed strong agreement with consensus readings, exceeding surgeon-to-surgeon consistency (ICC 0.84 vs 0.78 for all patients; ICC 0.71 vs 0.63 for low bone loss; ICC 0.83 vs 0.21 for high bone loss; P < 0.001). For the classification task of assigning each patient to different bone loss severity subgroups, the pipeline's sensitivity was 71.4% for the low-severity group and 85.7% for the high-severity group, with no instances of misclassifying low as high or vice versa. A fully automated, deep learning-based pipeline for glenoid bone-loss measurement on CT scans can be a clinically reliable tool to assist clinicians with preoperative planning for shoulder instability. We are releasing our model and dataset at https://github.com/Edenliu1/Auto-Glenoid-Measurement-DL-Pipeline .