Maxillary sinus floor augmentation (MSFA) is widely used and considered a predictable procedure for implant placement. However, the influence of MSFA on implant survival and marginal bone loss (MBL) is still inconclusive. The purpose of this retrospective observational study is to evaluate the long-term genuine influence of MSFA on the survival and MBL of implants by comparing those with and without MSFA only in maxillary molars within the same patients. Thirty-eight patients (28 male and 10 female), with a total of 119 implants, received implants with and without MSFA, and were followed up for 5.8 to 22 years. Patient- and implant-related factors were assessed with a frailty model for implant survival and with generalized estimation equations (GEE) for MBL around the implant. No variables showed a statistical significance for implant failure in the frailty model. In GEE analysis for MBL, MSFA did not show any statistical significance. In conclusion, MSFA demonstrated no significant influence on implant failure and MBL in posterior maxilla in this study.