Background Echocardiographic measurement of mitral valve area (MVA) is critical prior to percutaneous transmitral commissurotomy (PTMC). This study aimed to compare the agreement between transthoracic (TTE) and transesophageal echocardiography (TEE) in three‐dimensional (3D) planimetric measurement of the MVA among patients with severe mitral stenosis. Methods MVA was measured with planimetry in 105 patients before undergoing PTMC. 3D reconstruction was applied to both TTE and TEE examinations. The MVA values from four different methods of 3D reconstruction were compared to the average values of 3D methods in TEE as the gold standard measurement method for the MVA in this study. The agreement levels between the two examinations were evaluated and analyzed for various reconstruction methods. Results The mean age was 49 ± 12 years for 28 men and 77 women who were enrolled. The image quality was graded as “excellent” in 57% of 3D images obtained by TTE, while it was graded as “excellent” in 81% of 3D images obtained by TEE. The ventricular zooming method in TTE with a bias of −0.006 ± 0.065 cm2 (P < 0.0001) had the highest agreement with the 3D‐MVA in TEE. While 2D‐TTE and 3D‐TEE measurements of the MVA (R = 0.91; P < 0.0001) were significantly correlated, 2D‐TTE overestimated the MVA by 0.19 cm2. Conclusion Although the quality of 3D images was significantly better in TEE than those in TTE, a good agreement existed between the measured 3D‐TTE and 3D‐TEE studies. We also demonstrated that 2D‐TTE overestimated the MVA compare to 3D‐TEE.