In this paper, a frequency selective surface (FSS) based shared-aperture antenna is designed for 5G/Wi-Fi applications. The 5G and Wi-Fi channel are separated to achieve different polarizations and simultaneous work. The proposed antenna is of ±45°-polarization in the 5G N79 band and vertical polarization in the Wi-Fi5.8 GHz band. The antenna is vertically stacked with the N79 band antenna located above the Wi-Fi band antenna. The N79 antenna is composed of FSS units with transmissive characteristics in the Wi-Fi band, and serves as an electromagnetically transparent surface to avoid blocking the Wi-Fi antenna. A prototype of our design is fabricated, assembled and tested, and measured results show that the prototype is able to cover the entire N79 band (4.1–5.2 GHz, 23.7%) and Wi-Fi5.8 GHz band (5.73–5.89 GHz, 2.8%). Measured average gain is 8.2 and 7.8 dBi in the N79 and Wi-Fi band, respectively, and radiation efficiency is over 86 and 80%. The proposed design exhibits separated channels, tri-polarizations, high gain and compact size, which is sufficient for regular 5G/Wi-Fi applications. The antenna also achieves a relatively wide and highly consistent signal coverage in the two bands, making it suitable for 5G/Wi-Fi multi-function communication and indoor 5G blind compensation.