This dataset contains molybdenum isotope (δ⁹⁸Mo) compositions and elemental concentration data (Al, Fe, Mn, Mo) from two oxic pelagic sediment cores covering approximately 90 million years of sedimentation. The data were generated in 2023 and 2024. Core LL44-GPC3 (30.33, -157.83) was recovered from the North Pacific Gyre, and core U1366F (-26.05, -156.89) was recovered from the South Pacific Gyre. Both cores are characterised by oxygenated pore waters in their entire length. All analyses were performed at GEOMAR Helmholtz Centre for Ocean Research Kiel (Germany). Bulk sediment samples were analysed for δ⁹⁸Mo using multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS), while elemental concentrations were determined by ICP-OES and ICP-MS. The data document the variability of δ⁹⁸Mo in oxic marine sediments and can be used to support studies of molybdenum isotope systematics and sedimentary diagenesis in marine environments.