The submitted dataset belongs with a manuscript titled "Size-fraction-specific isotope variations as a framework to interpret early Eocene bulk sediment carbon isotope records" which is currently in revision in Paleoceanography and Paleoclimatology. Here we present changes in abundances and δ13C and δ18O composition of five size fractions of bulk sediments from ODP Site 1209 in Shatsky Rise, north-central Pacific, deposited BETWEEN 58-50 Ma. The dataset includes four tables. The bulk sediments were rinsed and segregated into five size fractions: <25 μm, 25-63 μm, 63-125 μm, 125-250 μm and >250 μm. The difference in mass of sediments before and after size-fraction separation is reported in the first sheet. The second sheet documents temporal changes in relative weights of the various size fractions: namely fine fraction (FF), intermediate fraction (IF), coarse fraction (CF) and the three sub-fractions of CF. The δ13C and δ18O composition of bulk sediments and size fractions are reported in the third and fourth sheets, respectively.