The study of deep-time ecological dynamics has the ability to inform conservation decisions by anticipating the behavior of ecosystems millions of years into the future. Using network analysis and an exceptional fossil dataset spanning the past 21 million years, we show that mammalian ecological assemblages undergo long periods of functional stasis, notwithstanding high taxonomic volatility due to dispersal, speciation, and extinction. Higher functional richness and diversity promoted the persistence of functional faunas despite species extinction risk being indistinguishable among these different faunas. These findings, and the large mismatch between functional and taxonomic successions, indicate that although safeguarding functional diversity may or may not minimize species losses, it would certainly enhance the persistence of ecosystem functioning in the face of future disturbances.