This dataset presents benthic foraminiferal δ¹⁸O chronostratigraphies and associated uncertainties for International Ocean Discovery Program (IODP) Site U1541, based on different tuning targets including LR04 (Lisiecki and Raymo, 2005), LR09 (Lisiecki and Raymo, 2009), CENOGRID (Westerhold et al., 2020) and Probstack (Ahn et al., 2017) and based on manual versus automated tuning techniques (Middleton et al., 2024). The benthic foraminiferal δ¹⁸O record for IODP Site U1541 (54°13'S, 125°25'W) recently recovered from the central South Pacific on IODP Expedition 383 (Winckler et al., 2021) is presented for the first time in Middleton et al. (2024). It is based on stable isotope analyses of Cibicidoides wuellerstorfi and Cibicides kullenbergi (Middleton et al., 2024), and was combined with the benthic foraminiferal δ¹⁸O record of PS75/059-2 (Ullermann et al., 2016). Automated tuning is based on Hidden Markov Model (HMM)-Match-based alignments (Middleton et al., 2024) generated using the automated probabilistic HMM-Match algorithm of Lin et al. (2014). The manual tuning was generated by visual alignment of characteristic peaks and troughs of the benthic foraminiferal δ¹⁸O record of IODP Site U1541 to the benthic foraminiferal LR04 stack using the publicly available QAnalySeries software (Kotov and Pälike, 2018). The dataset provides the basis for investigating and discussing the uncertainties of benthic foraminiferal δ¹⁸O stratigraphies for conventional manual and automated tuning techniques and evaluate their impact on sedimentary age models over the past 3.5 Myr (Middleton et al., 2024).