Sediment-hosted gold deposits in central Yukon have most of the diagnostic characteristics of Carlin-type gold deposits in Nevada. This study combines organic matter geothermometry with fluid inclusion microthermometry, clumped isotope data (Δ47) for late ore-stage hydrothermal calcite, and apatite fission-track analyses to constrain the thermal evolution of Carlin-type gold zones in central Yukon. The Tmax parameter derived from pyrolysis analyses indicates that organic matter is overmature and records regional temperatures of > 150 °C. Calcite and fluorite associated with the waning stage of mineralization at ca. 74 Ma have mean fluid inclusion homogenization temperatures of 123–173 °C, with an average salinity of 4.8 wt.% NaCl equiv. These temperatures overlap values of 91–162 °C determined from calcite clumped isotope measurements and are similar to data from Carlin-type deposits in Nevada. Fluid mixing is suggested by a variation of the isotopic composition of the fluid in equilibrium with calcite, with the higher temperature end-member having higher δ18OH2O values. In thermal models based on Tmax, fluid inclusion microthermometry, clumped isotope measurements, and apatite fission-track data, a higher temperature event at approximately 220 °C is consistent with pyrobitumen reflectance measurements. This event is either related to maximum tectonic burial prior to mineralization or to the flow of acidic hydrothermal fluids early in the main ore-stage. Each analytical technique used in this study is independent of the others and records part of the thermal and chemical evolution of the Yukon Carlin-type gold deposits and their host rocks.