The frequency and intensity of disturbance on living coral reefs have been accelerating for the past few decades, resulting in a changed seascape. What is unclear but vital for management is whether this acceleration is natural or coincident only with recent human impact. We surveyed nine uplifted early to mid-Holocene (11,000–3700 calendar [cal] yr B.P.) fringing and barrier reefs along ∼27 km at the Huon Peninsula, Papua New Guinea. We found evidence for several episodes of coral mass mortality, but frequency was <1 in 1500 yr. The most striking mortality event extends >16 km along the ancient coastline, occurred ca. 9100–9400 cal yr B.P., and is associated with a volcanic ash horizon. Recolonization of the reef surface and resumption of vertical reef accretion was rapid (<100 yr), but the post-disturbance reef communities contrasted with their pre-disturbance counterparts. Assessing the frequency, nature, and long-term ecological consequences of mass-mortality events in fossil coral reefs may provide important insights to guide management of modern reefs in this time of environmental degradation and change.