Fringing reefs are rare on the mid-shelf of the central Great Barrier Reef, with Holocene development histories established for a few examples. The paucity of reef growth records from mid-shelf fringing reefs has limited opportunities for comparisons with inshore fringing reef growth records to better understand the influence of changes in environmental conditions on reef growth with distance offshore. The long-term development of the mid-shelf fringing reef at Holbourne Island was reconstructed using nine percussion and drill cores that captured the entire Holocene period of reef growth. The cores were chronologically constrained by 16 high-precision 230Th ages. A weathered, Pleistocene reef substrate was U-Th dated as last interglacial (open system age of 131,100 ± 1000 cal yBP) and this provides the underlying foundation upon which the Holocene reef initiated prior to ~7520 ± 20 cal yBP. The last interglacial reef was encountered 5.9 m below the present reef surface and is the shallowest confirmed last interglacial reef in the central GBR region to date. Most of the Holocene reef structure was emplaced within 1000 years of initiation. The chronostratigraphy and contemporary geomorphology of the fringing reef at Holbourne Island preserve evidence of re-working and stripping of the reef structure by cyclones. This evidence includes: 1) an age hiatus in core data of ~3500 years (6238 ± 18 to 2683 ± 10 cal yBP); 2) the abundance of detrital branching coral rubble material within the core facies; 3) the surface elevations and ages of fossil microatolls, which reveal that storm-induced ponding of water during low tidal stages up to 55 cm deep has been active (but intermittent) across the reef flat for at least 600 years and is still active today; and 4) long-standing shingle ridges onshore and modern shingle ridges on the reef flat.