We aimed to compare the efficacy and safety of transcatheter aortic valve implantation (TAVI) using Edwards SAPIEN 3 (S3) valve and SAPIEN XT) in smaller anatomy. The new generation S3 TAVI device has been used worldwide; however, its efficacy and safety in smaller Asian anatomy remain unknown. Between February 2014 and March 2017, 166 consecutive patients (S3, 54; XT, 112) were treated with balloon-expandable TAVI in a single center and their outcomes were analyzed. Median patient age was 85 (range: 81–88) years and mean body surface area was 1.41 ± 0.15 m². A 23-mm size valve was used in S3 and XT groups (70 vs. 62%, p = 0.224). The transfemoral approach was more frequently used in the S3 than in the XT group (96 vs. 72%, p < 0.001). Although, the minimal luminal diameter of the femoral artery was smaller in the S3 group (5.9 vs. 6.4 mm, p = 0.001), the rates of major (2 vs. 11%, p = 0.226) and minor (11 vs. 5%, p = 0.107) vascular complications did not increase. The frequency of paravalvular leaks (PVL) ≥ 2 was significantly reduced in the S3 group (11 vs. 61%, p < 0.001); however, pre- (24 vs. 91%, p < 0.001) and post- (4 vs. 19%, p < 0.001) dilatations were less frequently performed. Pacemaker implantation incidence did not increase (4 vs. 5%, p = 1.0) and peak velocity of the transcatheter heart valve was significantly higher in the S3 group (2.3 vs. 2.2 m/s, p = 0.046). Device success was high (89 vs. 93%, p = 0.387) while the 30-day all-cause mortality was low (2 vs. 1%, p = 0.583) in both groups. TAVI with the S3 device was safe and effective, with low incidence of vascular complications and reduced PVL, in smaller body-sized Asians.