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Objectives: To systematically assess whether MRI-based measurements of glenoid bone loss (GBL) are comparable to CT in patients with shoulder instability. Methods: We searched PubMed, Cochrane Library, Web of Science, and Embase for studies comparing GBL measurements between CT and MRI through May 16, 2024. We performed subgroup analyses based on 2D versus 3D imaging and linear versus area measurement methods. We conducted statistical analysis using Review Manager (RevMan) version 5.4.1, applying a random-effects model to calculate the mean difference. Results: Eleven studies were included, totaling 492 shoulders. Of these, 119 shoulders were evaluated using 3D MRI versus 3D CT, 126 using 2D MRI versus 2D CT, 292 using the linear method, and 149 using the area method. The pooled analysis showed no significant difference in GBL measurements between MRI and CT (mean difference -0.05; 95% CI: -0.26 to 0.15; p = 0.61). Subgroup analyses also showed no significant differences (p = 0.94 for 3D, p = 0.14 for 2D, p = 0.67 for linear, p = 0.46 for area, and p = 0.51 comparing linear vs area methods). Conclusions: MRI provides GBL measurements comparable to CT across various imaging protocols including 2D and 3D approaches and the linear and area methods. MRI may be sufficient as the sole imaging modality for comprehensive preoperative evaluation in patients with shoulder instability.