Despite all the efforts to optimize the meniscus prosthesis system (geometry, material, and fixation type), the success of the prosthesis in clinical practice will depend on surgical factors such as intra-operative positioning of the prosthesis. In this study, the aim was therefore to assess the implications of positional changes of the medial meniscus prosthesis for knee biomechanics. A detailed validated finite element (FE) model of human intact and meniscal implanted knees was developed based on a series of in vitro experiments. Different non-anatomical prosthesis positions were applied in the FE model, and the biomechanical response during the gait stance phase compared with an anatomically positioned prosthesis, as well as meniscectomized and also the intact knee model. The results showed that an anatomical positioning of the medial meniscus prosthesis could better recover the intact knee biomechanics, while a non-anatomical positioning of the prosthesis to a limited extent alters the knee kinematics and articular contact pressure and increases the implantation failure risk. The outcomes indicate that a medial or anterior positioning of the meniscus prosthesis may be more forgiving than a posteriorly or laterally positioned prosthesis. The outcome of this study may provide a better insight into the possible consequences of meniscus prosthesis positioning errors for the patient and the prosthesis functionality.