An alternative solution to conventional stump–socket prosthetic limb attachment is offered by direct skeletal fixation. This study aimed to assess two percutaneous trans-femoral implants, the OPRA system (Integrum AB, Göteborg, Sweden), and the ISP Endo/Exo prosthesis (ESKA Implants AG, Lübeck, Germany) on bone failure and stem–bone interface mechanics both early post-operative (before bony ingrowth) and after full bone ingrowth. Moreover, mechanical consequences of implantation of those implants in terms of changed loading pattern within the bone and potential consequences on long-term bone remodeling were studied using finite-element models that represent the intact femur and implants fitted in amputated femora. Two experimentally measured loads from the normal walking cycle were applied. The analyses revealed that implantation of percutaneous prostheses had considerable effects on stress and strain energy density levels in bone. This was not only caused by the implant itself, but also by changed loading conditions in the amputated leg. The ISP design promoted slightly more physiological strain energy distribution (favoring long-term bone maintenance), but the OPRA design generated lower bone stresses (reducing bone fracture risk). The safety factor against mechanical failure of the two percutaneous designs was relatively low, which could be improved by design optimization of the implants.