Abstract Background Membranous interventricular septum aneurysm (MISA) is a rare abnormality occurring in 0.3% of patients with congenital heart disease, which thereby increases anatomical complexity. Case summary Transcatheter aortic valve replacement (TAVR) procedure was planned for a 71-year-old female patient from East Asia with a type 1 bicuspid aortic valve diagnosed with severe aortic stenosis by transthoracic echocardiography (TTE). Preprocedural multidetector computed tomography (MDCT) clearly revealed an extremely horizontal aorta and a MISA originating from the sub-annulus with the upper edge extending 7.2 mm above the annulus. A probable communicating flow between the left ventricle and the aorta was confirmed by reviewing the TTE images. Moreover, there was a calcified raphe between the left- and right-coronary cusps. A downsized balloon expandable valve (a 23mm Sapien 3 valve with an additional 2 ml dilation) was therefore chosen and deployed with a 100/0 aortic/ventricular ratio position. The TTE post-implantation indicated a trace perivalvular leakage. The cardiac MDCT performed post-procedure, at the 6-month and 12-month follow-ups demonstrated complete sealing and significant healing of the aneurysm. Discussion Transcatheter aortic valve replacement utilizing a balloon-expandable valve was successfully performed for a case with membranous interventricular septum aneurysm extending above the annulus. Comprehensive imaging analysis before the procedure is crucial for TAVR with challenging anatomical conditions.