Temperature reconstructions indicate that the Pliocene was ~3 degrees C warmer globally than today, and several recent reconstructions of Pliocene atmospheric CO2 indicate that it was above pre-industrial levels and similar to those likely to be seen this century. However, many of these reconstructions have been of relatively low temporal resolution, meaning that these records may have failed to capture variations associated with the 41 Kyr glacial-interglacial cycles thought to operate in the Pliocene. These data represent new, high temporal resolution alkenone carbon isotope based record of pCO2 spanning 0 to 0.2 and 2.6 to 3.3 million years ago from ODP Site 999 (supplementing our other data repository focused on 2.8 to 3.3 million years ago). Our record allows a) direct comparison of alkenone-derived pCO2 from the Pleistocene to that of the Pliocene and b) comparison of the former to the ice core record. The raw data are sea surface temperature estimates from the Uk'37 proxy, foraminiferal and alkenone d13C values, from which carbon isotope fractionation during photosynthesis (ep) can be calculated. Using nutrient concentrations (growth rate correction) and SSTs, these ep values can be converted into [CO2(aq)] which in turn can be used to calculate pCO2.