Piston stapes prostheses are implanted in patients with refractory conductive or mixed hearing loss due to stapes otosclerosis to stimulate the perilymph with varying degrees of success. The overclosure effect described by the majority of researchers affects mainly low and medium frequencies, and a large number of patients report a lack of satisfactory results for frequencies above 2 kHz. The mechanics of perilymph stimulation with the piston have not been studied in a systematic manner. The objective of this study was to assess the influence of stapedotomy surgery on round window membrane vibration and to estimate the postoperative outcomes using the finite element (FE) method. The study hypothesis is that the three-dimensional FE model developed of the human inner ear, which simulates the round window (RW) membrane vibration, can be used to assess the influence of stapedotomy on auditory outcomes achieved after the surgical procedure. An additional objective of the study was to enable the simulation of RW membrane vibration after stapedotomy using a new type of stapes prosthesis currently under investigation at Warsaw University of Technology. A three-dimensional finite element (FE) model of the human inner ear was developed and validated using experimental data. The model was then used to simulate the round window membrane vibration before and after stapedotomy surgery. Functional alterations of the RW membrane vibration were derived from the model and compared with the results of experimental measurements from temporal bones of a human cadaver. Piston stapes prosthesis implantation causes an approximately fivefold (14 dB) lower amplitude of the RW membrane vibrations compared with normal anatomical conditions. A satisfactory agreement between the FE model and the experimental data was found. The new prosthesis caused an increase of 20–30 dB in the RW displacement amplitude compared with the 0.4-mm piston prosthesis. In all frequencies, the FE model predicted a RW displacement curve that was above the experimental curves for the normal ear. The stapedotomy can be well simulated by the FE model to predict the auditory outcomes achieved following this otosurgery procedure. The 3D FE model developed in this study may be used to optimize the geometry of a new type of stapes prosthesis in order to achieve a similar sound transmission through the inner ear as for a normal middle ear. This should provide better auditory outcomes for patients with stapedial otosclerosis.