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Objective: Internal Jugular Vein Stenosis (IJVS) is hypothesized to play a role in the pathogenesis of diverse neurological diseases. We sought to evaluate differences in IJVS assessment between CT and MRI in a retrospective patient cohort. Methods: We included consecutive patients who had both MRI of the brain and CT of the head and neck with contrast from 1 June 2021 to 30 June 2022 within the same admission. The degree of IJVS was categorized into five grades (0–IV). Results: A total of 35 patients with a total of 70 internal jugular (IJ) veins were included in our analysis. There was fair intermodality agreement in stenosis grades (κ = 0.220, 95% C.I. = [0.029, 0.410]), though categorical stenosis grades were significantly discordant between imaging modalities, with higher grades more frequent in MRI (χ² = 27.378, <i>p</i> = 0.002). On CT-based imaging, Grade III or IV stenoses were noted in 17/70 (24.2%) IJs, whereas on MRI-based imaging, Grade III or IV stenoses were found in 40/70 (57.1%) IJs. Among veins with Grade I-IV IJVS, MRI stenosis estimates were significantly higher than CT stenosis estimates (77.0%, 95% C.I. [35.9–55.2%] vs. 45.6%, 95% C.I. [35.9–55.2%], <i>p</i> < 0.001). Conclusion: MRI with contrast overestimates the degree of IJVS compared to CT with contrast. Consideration of this discrepancy should be considered in diagnosis and treatment planning in patients with potential IJVS-related symptoms.