The objective of this study was to perform a comparative evaluation of the radiographic outcomes of lateral sinus floor elevation with and without bone window repositioning (BLSFE and LSFE, respectively) when applied concomitantly with implant placement. A randomized controlled clinical trial was conducted between February 1, 2016 and May 1, 2017 including 26 individuals with at least one missing tooth. Participants were randomized 1:1 to undergo BLSFE (10 participants, 16 implants) or LSFE (13 participants, 19 implants). Bovine-derived xenograft was used in both groups and the implants were inserted concomitantly. In the BLSFE group, the antrostomy was covered with a repositioned bone window and then with a concentrated growth factors (CGF) membrane. In the LSFE group, the antrostomy was covered with a CGF membrane. Panoramic radiographs were taken before surgery (T0), immediately postoperative (T1), and at 12 months postoperative (6 months after loading) (T2). Marginal bone loss (MBL), apical bone gain, augmented alveolar bone height, and intra-sinus bone augmentation were evaluated on panoramic radiographs at T2. A linear regression analysis with generalized estimating equation models was performed. The implant survival rate was 100% at 1 year after implant surgery. The residual alveolar bone height at T0 was comparable in the BLSFE and LSFE groups (3.58 ± 1.49 mm vs 4.12 ± 1.61, P = 0.32), as was the alveolar bone height at T1 (13.61 ± 1.82 mm vs 12.38 ± 1.82 mm, P = 0.06). At T2, significantly higher alveolar bone height, intra-sinus bone augmentation, and apical bone gain, and lower distal MBL were observed in the BLSFE group when compared to the LSFE group, with adjusting for covariates (β = 2.44, 95% CI 1.42–3.46, P < 0.0001; β = 2.38, 95% CI 1.35–3.41, P < 0.0001; β = 2.33, 95% CI 1.23–3.42, P < 0.0001; and β = −0.43, 95% CI −0.83 to −0.02, P = 0.038, respectively). No significant difference was observed for mesial MBL or apical bone resorption at T2. Lateral sinus floor elevation with bone window repositioning may result in higher bone augmentation after 1 year than the traditional approach. Further research is needed to elucidate the effect of lateral sinus floor elevation with bone window repositioning.