Reef response to Last Interglacial (LIG) sea level and palaeoenvironmental change has been well documented at a limited number of far-field sites remote from former ice sheets. However, the age and development of LIG reefs in the Great Barrier Reef (GBR) remain poorly understood due to their location beneath modern living reefs. Here we report thirty-nine new mass spectrometry U-Th ages from seven LIG platform reefs across the northern, central and southern GBR. Two distinct geochemical populations of corals were observed, displaying activity ratios consistent with either closed or open system evolution. Our closed-system ages (~129–126ka) provide the first reliable LIG ages for the entire GBR. Combined with our open-system model ages, we are able to constrain the interval of significant LIG reef growth in the southern GBR to between ~129–121ka. Using age-elevation data in conjunction with newly defined coralgal assemblages and sedimentary facies analysis we have defined three distinct phases of LIG reef development in response to major sea level and oceanographic changes. These phases include: Phase 1 (>129ka), a shallow-water coralgal colonisation phase following initial flooding of the older, likely Marine Isotope Stage 7 (MIS7) antecedent platform; Phase 2 (~129ka), a near drowning event in response to rapid sea level rise and greater nutrient-rich upwelling and; Phase 3 (~128–121ka), establishment of significant reef framework through catch-up reef growth, initially characterised by deeper, more turbid coralgal assemblages (Phase 3a) that transition to shallow-water assemblages following sea level stabilisation (Phase 3b). Coralgal assemblage analysis indicates that the palaeoenvironments during initial reef growth phases (1 and 2) of the LIG were significantly different than the initial reef growth phases in the Holocene. However, the similar composition of ultimate shallow-water coralgal assemblages and slow reef accretion rates following stabilisation of sea level (phase 3b) suggest that reefs of both ages developed in a similar way during the main phase of relatively stable sea level.