An end-fire radiating implantable antenna with a small footprint and broadband operation at the frequency range of 3–5 GHz is proposed for high-data-rate wireless communication in a brain–machine interface. The proposed Vivaldi antenna was implanted vertically along the height of the skull to avoid deformation in the radiation pattern and to compensate for a gain–loss caused by surrounding lossy brain tissues. It was shown that the vertically implanted end-fire antenna had a 3 dB higher antenna gain than a horizontally implanted broadside radiating antenna discussed in recent literature. Additionally, comb-shaped slot arrays imprinted on the Vivaldi antenna lowered the resonant frequency by approximately 2 GHz and improved the antenna gain by more than 2 dB compared to an ordinary Vivaldi antenna. An antenna prototype was fabricated and then tested for verification inside a seven-layered semi-solid brain phantom where each layer had similar electromagnetic material properties as actual brain tissues. The measured data showed that the antenna radiated toward the end-fire direction with an average gain of −15.7 dBi under the frequency of interest, 3–5 GHz. A link budget analysis shows that reliable wireless communication can be achieved over a distance of 10.8 cm despite the electromagnetically harsh environment.