Fluorescence-lifetime imaging microscopy (FLIM) is a powerful technique for highly multiplexed imaging in live cells. In this work, we present a genetically encoded FLIM multiplexing platform based on a combination of fluorogen-activating protein FAST and red-shifted fluorogen from the arylidene-imidazolone family. We showed that a series of FAST protein mutants exhibit similar steady-state optical properties in complex with fluorogen but have different fluorescence lifetimes. The similar brightness and binding strength of pairs of these FAST protein variants with allows them to be successfully used for multiplexing up to three intracellular structures of living cells simultaneously.