The theoretical prediction of Earth-Moon dynamics in deep geologic time is hampered by limited knowledge of Earth's past tidal dissipation and dynamical ellipticity. Cyclostratigraphy can, however, provide valuable information on the geologic evolution of the Earth-Moon dynamical parameters. Here we investigate Eocene cyclostratigraphy to estimate Earth's precession rate (p), Earth-Moon distance (EMD) and length-of-day (LOD). Two highly-resolved deep sea records are selected from the Atlantic Ocean, with ages centered on 42.5 Ma (40.9–44.3 Ma; IODP Site U1410) and 54.95 Ma (54.1–55.8 Ma; ODP Site 1262). The sedimentary sequences at these sites recorded Milankovitch forcing signals with prominent precession index (Site 1262) and obliquity (Site U1410) frequencies and their amplitude modulations. At Site U1410, amplitude modulation of the main obliquity cycle was tuned to the Earth's 173-kyr orbital inclination (s3-s6) metronome, and at Site 1262, the dominant precession index amplitude modulation to the 405-kyr orbital eccentricity (g2-g5) metronome. This enabled estimation of Earth's precession rate p of 51.486 ± 0.064 arcsec/yr and 51.546 ± 0.168 arcsec/yr for 42.5 Ma and 54.95 Ma, respectively. These p estimates indicate EMD values of 383.710 ± 0.090 × 103 km and 382.625 ± 0.265 × 103 km, and LOD values of 23.679 ± 0.0115 h and 23.667 ± 0.039 h for 42.5 Ma and 54.95 Ma, respectively. These estimates deviate from theoretical predictions based on back calculation assuming present-day tidal dissipation. In particular, a significant discrepancy between the model and observations (cyclostratigraphy) occurs at 54.95 Ma (Site 1262) suggesting contributions from other effects on Earth's rotation, including changes in tidal dissipation and/or Earth's dynamical ellipticity related to mantle convection and the early Eocene global warming.