The subantarctic islands between 40 and 60°S are circum-polar landmasses influenced by the southern westerly wind (SWW) belt whose latitudinal shifts are driven by the Southern Annular Mode (SAM) over decadal timescales. In the Indian sector of the Southern Ocean, the Kerguelen Islands (49°S) form a volcanic archipelago that is home to the Cook Ice Cap (CIC). Atmospheric drying favored by a poleward migration of the SWW induced a dramatic shrinkage of the CIC over the past 50 years. Current knowledge of how this decline compares with the natural variability of the CIC is unclear and based exclusively on geomorphological records with limited temporal resolution. This paper introduces a 4 kyr marine record built from a transect of giant piston cores collected in Table Fjord, southwestern margin of the CIC. Interpretation of sedimentary and geochemical proxies is supported by statistical correlations with the CIC surface mass balance on the instrumental timescale, and by the age overlapping with dated landforms and deposits over the last two millennia. High-resolution geochronological data (137Cs and 210Pb inventories along with 63 AMS 14C dates) corrected from a local marine reservoir age allowed reconstructing glacier variability at a multidecadal resolution. The CIC was paced by periods of glacial advances at 3.4–2.8, 2.3–1.7, and 1.35–1.15 ka cal BP, followed by a two-stage ‘Little Ice Age’ maximum between 0.7 ka cal BP and the early 20th century. Comparison with paleoenvironmental records from the subantarctic fringe zone and the southern mid-latitudes suggests SWW-driven precipitation (wetter and windier conditions) were the main driver of centennial-scale glacier variability in the Kerguelen Islands, notably after 2.3 ka cal BP. The Kerguelen record thereby supports a zonally-synchronous, hemispheric-wide SWW pattern pacing Southern Ocean climatic variability in a SAM-like mode. The Little Ice Age maximum ice extent results from the coincidence of cold conditions caused by an equatorward shift of the Polar Front, an oceanic front bordering the Kerguelen archipelago resulting in lower sea surface temperatures, together with wetter conditions favored by strengthened SWW.