Paleoceanographic interpretations of Plio-Pleistocene climate variability over the past 5 million years rely on the evaluation of event timing of proxy changes in sparse records across multiple ocean basins. In turn, orbital-scale chronostratigraphic controls for these records are often built from stratigraphic alignment of benthic foraminiferal stable oxygen isotope (δ18O) records to a preferred dated target stack or composite. This chronostratigraphic age model approach yields age model uncertainties associated with alignment method, target selection, the assumption that the undated record and target experienced synchronous changes in benthic foraminiferal δ18O values, and the assumption that any possible stratigraphic discontinuities within the undated record have been appropriately identified. However, these age model uncertainties and their impact on paleoceanographic interpretations are seldom reported or discussed. Here, we investigate and discuss these uncertainties for conventional manual and automated tuning techniques based on benthic foraminiferal δ18O records and evaluate their impact on sedimentary age models over the past 3.5g Myr using three sedimentary benthic foraminiferal δ18O records as case studies. In one case study, we present a new benthic foraminiferal δ18O record for International Ocean Discovery Program (IODP) Site U1541 (54°13′g S, 125°25′g W), recently recovered from the South Pacific on IODP Expedition 383. The other two case studies examine published benthic foraminiferal δ18O records of Ocean Drilling Program (ODP) Site 1090 and the ODP Site 980/981 composite. Our analysis suggests average age uncertainties of 3 to 5g kyr associated with manually derived versus automated alignment, 1 to 3g kyr associated with automated probabilistic alignment itself, and 2 to 6g kyr associated with the choice of tuning target. Age uncertainties are higher near stratigraphic segment ends and where local benthic foraminiferal δ18O stratigraphy differs from the tuning target. We conclude with recommendations for community best practices for the development and characterization of age uncertainty of sediment core chronostratigraphies based on benthic foraminiferal δ18O records.