In the Precambrian, reverse weathering—a process consuming oceanic silica, metal cations and alkalinity to form marine clays—was a key control of the long-term carbon cycle. However, the appearance of marine silicifiers decreased the importance of this process in regulating climate in the Phanerozoic eon. Here, we present seawater lithium and strontium isotope records derived from bulk carbonates and fossil brachiopods spanning the Permian to Early Triassic, an interval of pronounced climatic fluctuations and widespread extinctions. We show that the lithium isotope composition of seawater remained constant for most of the Permian until a sharp decrease in the late Permian (~254 Myr ago) with low seawater Li isotope values (~10‰) persisting throughout the Early Triassic. Based on box modelling, changes in chemical weathering and hydrothermal fluxes are unable to explain the abrupt decline in seawater Li isotopes. Rather, increased lithium output fluxes through enhanced reverse weathering are required to produce the low Li isotope values of the late Permian and Early Triassic (253–247 Myr ago). Increased reverse weathering rates could explain the failure of chemical weathering to draw down atmospheric CO₂ levels during the Early Triassic, leading to protracted biotic recovery from the Permian–Triassic mass extinction.