Northern Hemisphere-wide cooling during the Little Ice Age (LIA; CE 1650-1775) is associated with a ~5 ppmv decrease in atmospheric carbon dioxide. Changes in terrestrial and ocean carbon reservoirs have been postulated as possible drivers of this relatively large shift in atmospheric CO₂, potentially providing insights into the mechanisms and sensitivity of the global carbon cycle. Here we report decadally-resolved radiocarbon (¹⁴C) levels in a network of tree rings series spanning CE 1700-1950 located along the northern boundary of, and within, the Southern Ocean. We observe regional dilutions in atmospheric radiocarbon (relative to the Northern Hemisphere) associated with upwelling of ¹⁴CO₂–depleted abyssal waters. We find the inter-hemispheric ¹⁴C offset approaches zero during increasing global atmospheric CO₂ at the end of the LIA, with reduced ventilation in the Southern Ocean and a Northern Hemisphere source of old carbon (most probably originating from deep Arctic peat layers). The coincidence of the atmospheric CO₂ increase and reduction in the inter-hemispheric ¹⁴C offset imply a common climate control. Possible mechanisms of synchronous change in the high latitudes of both hemispheres are discussed.