Constraints on the evolution of atmospheric CO₂ levels throughout Earth’s history are foundational to our understanding of past variations in climate. Despite considerable effort, records vary in their temporal and spatial coverage and estimates of past CO₂ levels do not always converge, and therefore new records and proxies are valuable. Here we reconstruct atmospheric CO₂ values across major climate transitions over the past 16 million years using the boron isotopic composition (δ¹¹B) of planktic foraminifera from 89 samples obtained from two sites in the West Pacific Warm Pool, Ocean Drilling Program (ODP) Sites 806 and 807, measured using high-precision multi-collector inductively coupled plasma mass spectrometry. We compare our results to published data from ODP Site 872, also in the Western Equatorial Pacific, that goes back to 22 million years ago. These sites are in a region that today is near equilibrium with the atmosphere and are thought to have been in equilibrium with the atmosphere for the interval studied. We show that δ¹¹B data from this region are consistent with other boron-based studies. The data show evidence for elevated pCO₂ during the Middle Miocene and Early to Middle Pliocene, and reductions in pCO₂ of ∼200 ppm during the Middle Miocene Climate Transition, ∼250 ppm during Pliocene Glacial Intensification and ∼50 ppm during the Mid-Pleistocene Climate Transition. During the Mid-Pleistocene Transition there is a minimum pCO₂ at marine isotopic stage (MIS) 30. Our results are consistent with a coupling between pCO₂, temperature and ice sheet expansion from the Miocene to the late Quaternary.