Polymers for implantable devices are desirable for biomedical engineering applications. This study introduces a water-resistant, self-healing fluoroelastomer (SHFE) as an encapsulation material for antennas. The SHFE exhibits a tissue-like modulus (approximately 0.4 MPa), stretchability (at least 450%, even after self-healing in an underwater environment), self-healability, and water resistance (WVTR result: 17.8610 g m⁻² day⁻¹). Further, the SHFE is self-healing in underwater environments via dipole–dipole interactions, such that devices can be protected from the penetration of biofluids and withstand external damage. With the combination of the SHFE and antennas designed to operate inside the body, we fabricated implantable, wireless antennas that can transmit information from inside the body to a reader coil that is outside. For antennas designed considering the dielectric constant, the uniformity of the encapsulation layer is crucial. A uniform and homogeneous interface is formed by simply overlapping two films. This study demonstrated the possibility of wireless communication in vivo through experiments on rodents for 4 weeks, maintaining the maximum communication distance (15 mm) without chemical or physical deformation in the SHFE layer. This study illustrates the applicability of fluoroelastomers in vivo and is expected to contribute to realizing the stable operation of high-performance implantable devices.