The stable oxygen and clumped isotope composition of brachiopod calcite are important proxies for the reconstruction of Phanerozoic seawater temperatures and δ18O values. The utility of brachiopods as a temperature archive is nonetheless challenged by indications that their shells precipitate out of isotopic equilibrium with ambient seawater, though the origin of disequilibrium effects has remained elusive. Here, we apply the recently developed dual clumped isotope thermometer (i.e., the simultaneous measurement of Δ47 and Δ48 values in CO2 derived from the acid digestion of carbonates) to modern and fossil brachiopods to investigate disequilibrium signatures recorded in brachiopod calcite. We present evidence that disequilibrium signatures are derived from the combination of two rate-limiting processes: the hydration/hydroxylation of CO2, and, potentially, the diffusion of HCO3−/CO32− in water. An empirical correction for clumped isotope disequilibrium is presented, based on correlation between measured disequilibrium offsets in the Δ47 and Δ48 values of modern brachiopods (Δ47disequilibrium = –0.88 × Δ48disequilibrium + 0.02). Dual clumped isotope thermometry of Eocene age brachiopods from Seymour Island (∼65 °S) yields temperatures in agreement with previously reported Δ47 derived temperatures from coeval bivalves. In contrast, uncorrected Δ47 derived temperatures from the same brachiopods are 6–11 °C colder. Measurement of dual clumped isotope composition alongside δ18O values of brachiopod carbonate should also enable more accurate reconstruction of seawater-δ18O. In comparison with group-specific Δ47-temperature calibrations, which correct for an average kinetic bias in Δ47, dual clumped isotope thermometry accounts for the magnitude of disequilibrium inherent to an individual sample, facilitating more reliable paleotemperature and seawater-δ18O reconstructions.