Abstract The Southern Annular Mode (SAM) is the leading mode of atmospheric variability in the extratropical Southern Hemisphere and has wide ranging effects on ecosystems and societies. Despite the SAM’s importance, paleoclimate reconstructions disagree on its variability and trends. Here, we use data assimilation to reconstruct the SAM over the last 2000 years using temperature and drought-sensitive climate proxies. Our method does not assume a stationary relationship between proxy records and the SAM over an instrumental calibration period, so our reconstruction is less sensitive to the teleconnection variability that has hindered previous reconstructions. Our approach also allows us to identify critical paleoclimate records and quantify reconstruction uncertainty through time. We find no evidence for a forced response in SAM variability prior to the 20th century. We also find the modern positive trend is outside the range of the prior 2000 years, but only on multidecadal time scales.