Detailed temperature reconstructions over the past 2000 years are important for contextualising modern climate change. The mid‐latitude SE Pacific is a key region in this regard in terms of understanding the climatic linkages between the tropics and southern high latitudes. Multi‐centennial timescale temperature variability remains, however, poorly understood, due to a lack of long, high‐temporal‐resolution temperature records from this region and from the southern high latitudes in general. We present a unique alkenone sea surface temperature (SST) record from 44°S on the southern Chilean margin in the SE Pacific spanning the last 2300 years at decadal resolution. The record displays relatively large changes including a cooling transition from 14°C to 12.5°C between 1100 and 600 cal yrs BP, in line with other Chile margin SST records and coeval with Antarctic cooling. This cooling is attributable to reduced Southern Ocean deep convection, driven by a late Holocene sea‐ice increase in the Weddell Sea associated with increased El‐Niño Southern Oscillation (ENSO) variability. Superimposed on the late Holocene cooling we observe multi‐centennial timescale SST variability, including relatively cool SSTs (12.5°C) from 950 to 500 cal yrs BP, corresponding to the Medieval Climate Anomaly, and warmer SSTs (13°C) from 500 to 200 cal yrs BP, corresponding to the Little Ice Age. These oscillations may reflect either multi‐centennial internal variability of the Southern Ocean deep convection and/or multi‐centennial variability in the phasing of ENSO and Southern Annular Mode (SAM) events.