Ongoing retreat of Antarctica’s marine-based glaciers is associated with warm (~2° C) modified Circumpolar Deep Water intrusion onto the continental shelf, suggesting that Southern Ocean temperatures may influence Antarctic ice sheet stability. Understanding past cryosphere response to environmental forcing is crucial to modeling future ice sheet behavior. Of particular interest is the response of the East Antarctic Ice Sheet (EAIS), which stands to contribute ~20 m to global sea level. However, marine sediment sequences recording timing and variability of EAIS fluctuations through the last major climate shift, the Last Glacial Maximum (LGM), are either missing from the margin or have poor chronological control. Here we present three marine sediment cores that contain a record of pre-LGM fluctuations of the marine-based Lambert Glacier-Amery Ice Shelf (LG-AIS) system into Prydz Channel, East Antarctica. Analyses of core lithology, physical properties, cosmogenic nuclide concentration and diatom assemblage demonstrate that Prydz Channel was characterized by alternating open-marine and sub-shelf deposition, implying repeated LG-AIS fluctuations through the LGM. Our radiocarbon chronology demonstrates that LG-AIS fluctuations occurred on millennial timescales. Our record corroborates regional marine and terrestrial records, which demonstrate millennial scale variability in Antarctic Circumpolar Current strength, ice-rafted debris deposition, sea ice extent, Antarctic atmospheric temperature, and Southern Ocean sea surface temperature. This evidence suggests that the EAIS was sensitive to sub-orbital climate forcing in the past, and has implications for modeling future EAIS behavior.