Implantable electronic medical devices (IEMDs) can potentially be used to solve various clinical problems including the monitoring of chronic diseases and electro-organ transplantation. Several recently introduced techniques based on implantable devices that exploit novel metal- or carbon-based hybrid materials are biocompatible owing to their encapsulation in nontoxic polymers. However, such techniques limit the correct functioning of implantable devices, resulting in frequent replacement, difficult miniaturization, and inflammatory side effects in the body. Here, we describe a new technique for application to IEMDs that is capable of providing energy storage using the natural ions of body fluids as electrolytes in a supercapacitor (or ultracapacitor). The system is constructed with a solar cell for energy harvesting and a supercapacitor for energy storage. We assembled IEMDs with two biocompatible electrodes, specifically, MnO2 nanoparticles affixed to multi-walled carbon nanotubes as the positive electrodes and phosphidated activated carbon as the negative electrodes. From the obtained result, this work can be further extended to the use of rats. This technique avoids the problems of performance degradation and toxicity that normally limits the reaction that is permissible in extracellular fluid. We present this concept schematically. The two biocompatible electrodes were successfully implanted into the subcutaneous layer of a rat's skin with both electrodes showing stable performance in use as parts of a supercapacitor. These findings establish a platform for potential biocompatible materials for implantable energy storage devices.