An outstanding problem in our understanding of the global carbon cycle is unravelling the processes that were responsible for the rise of atmospheric CO2 during the last deglaciation (~19 to 11 ka). The carbon isotope 13C is commonly used to attribute the last deglacial atmospheric CO2 rise to various processes. The growth of tropical coral reefs has been controversially discussed in this context. To test this, well constrained reef carbonate records that span the last deglaciation are necessary, but such records are generally not available. Here we make use of a multi-proxy coral reef record obtained at the Great Barrier Reef by IODP Expedition 325. We show that the growth of the world’s largest reef system, the Great Barrier Reef, is marked by a pronounced decrease in δ13C in absolutely dated fossil coral skeletons between 12.8 and 11.7 ka, which coincides with a prominent minimum in atmospheric δ13CO2 and the Younger Dryas cold period of the Northern Hemisphere. The event follows the flooding of a large shelf platform and initiation of an extensive barrier reef system at 13 ka. We show, by carbon cycle simulations, that the Great Barrier Reef coral δ13C decrease was mainly caused by the combination of isotopic fractionation during reef carbonate production and the decomposition of organic land carbon on the newly flooded shallow-water platform. The impacts of these processes on atmospheric CO2 and δ13CO2, however, are marginal. Thus, the Great Barrier Reef was not contributing to the last deglacial δ13CO2 minimum at ~12.4 ka, and the world’s largest reef system in existence appears to have little effect on the last deglacial atmospheric CO2 and δ13CO2 changes.