Although temporal inconsistency in vertical deformation between long-term (> 103 years) uplift and short-term (101-102 years) subsidence along the Pacific coast of northeast Japan has been discussed in relation to cycles of megathrust earthquakes by some researchers, the fragmentary distribution of Pleistocene marine terraces and sparsity of studies on Holocene coastal geology indicate a lack of data on long-term vertical deformation at the occurrence of the 2011 Tohoku-oki earthquake. Recent geological studies along the northern Pacific coast (Sanriku coast), which were conducted after the 2011 earthquake, contribute to considerations of temporal inconsistency by providing new data on long-term vertical deformation. However, such studies have not been completed for the southern part of the coast. Millennial-scale vertical deformation at the Mano River Lowland, on the southern Pacific coast of northeast Japan is studied on the basis of well-dated Holocene sediment cores and existing boring logs. Subsurface geology documents the transgression and regression of the back-barrier estuary in the wave-dominated estuary system during the Holocene. The low relative sea-level (RSL) in the Early and Middle Holocene inferred from heights of marsh and intertidal sediments relative to non-tectonic hydro-isostatic sea-level predictions indicates a millennial-scale trend of subsidence at the Mano River Lowland. However, RSL in the Middle Holocene at the study area estimated from the sedimentary environment at that time is higher than that in the Tsugaruishi plain, northern Pacific coast of northeast Japan, where a millennial-scale subsidence of 1.1-1.9 mm/yr was previously inferred. This indicates that the Mano River lowland has been uplifted relative to the Tsugaruishi plain on a millennial scale. In combination with the deformation trend inferred from the distribution of the MIS 5.5 marine terrace, a change in the vertical deformation trend from stable or slight uplift to slight subsidence is implied to occur in the Mano River Lowland sometime between Late Pleistocene and Early Holocene.