(1) Background: We performed this study to evaluate the agreement between novel automated software of three-dimensional transesophageal echocardiography (3D-TEE) and multidetector computed tomography (MDCT) for aortic annular measurements of preprocedural transcatheter aortic valve replacement (TAVR); (2) Methods: PubMed, EMBASE, Web of Science, and Cochrane Library (Wiley) databases were systematically searched for studies that compared 3D-TEE and MDCT as the reference standard for aortic annular measurement of the following parameters: annular area, annular perimeter, area derived-diameter, perimeter derived-diameter, maximum and minimum diameter. Meta-analytic methods were utilized to determine the pooled correlations and mean differences between 3D-TEE and MDCT. Heterogeneity and publication bias were also assessed. Meta-regression analyses were performed based on the potential factors affecting the correlation of aortic annular area; (3) Results: A total of 889 patients from 10 studies were included in the meta-analysis. Pooled correlation coefficients between 3D-TEE and MDCT of annulus area, perimeter, area derived-diameter, perimeter derived-diameter, maximum and minimum diameter measurements were strong 0.89 (95% CI: 0.84–0.92), 0.88 (95% CI: 0.83–0.92), 0.87 (95% CI: 0.77–0.93), 0.87 (95% CI: 0.77–0.93), 0.79 (95% CI: 0.64–0.87), and 0.75 (95% CI: 0.61–0.84) (Overall p < 0.0001), respectively. Pooled mean differences between 3D-TEE and MDCT of annulus area, perimeter, area derived-diameter, perimeter derived-diameter, maximum and minimum diameter measurements were −20.01 mm2 ((95% CI: −35.37 to −0.64), p = 0.011), −2.31 mm ((95% CI: −3.31 to −1.31), p < 0.0001), −0.22 mm ((95% CI: −0.73 to 0.29), p = 0.40), −0.47 mm ((95% CI: −1.06 to 0.12), p = 0.12), −1.36 mm ((95% CI: −2.43 to −0.30), p = 0.012), and 0.31 mm ((95% CI: −0.15 to 0.77), p = 0.18), respectively. There were no statistically significant associations with the baseline patient characteristics of sex, age, left ventricular ejection fraction, mean transaortic gradient, and aortic valve area to the correlation between 3D-TEE and MDCT for aortic annular area sizing; (4) Conclusions: The present study implies that 3D-TEE using novel software tools, automatically analysis, is feasible to MDCT for annulus sizing in clinical practice.