Alkenone concentration data, Uk'37 ratios, Uk'37 temperature estimates, TEX86 ratios, and TEX86 temperature estimates were generated from ODP Site 846 (3307 m water depth) in the Eastern Equatorial Pacific for the interval from 5.1 Ma to 6 Ma at ~ 2.5 kyr resolution. Sediment samples were extracted using accelerated solvent extraction (ASE). Alkenone concentrations and ratios were measured using GC-FID. Isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) were measured using HPLC-MSD. Uk'37 temperature estimates are reported on both the Müller et al. (1998) and BAYSPLINE (Tierney & Tingley, 2018) calibrations. TEX86 temperature estimates are reported using the Kim et al. (2008), Kim et al. (2010), and BAYSPAR (Tierney and Tingley, 2014) calibrations. These data enable a comparison of temperature estimates from the Uk'37 and TEX86 paleothermometers.