Passive margin highlands occur on most continents on Earth and play a critical role in the cycle of weathering, erosion, and atmospheric circulation. Yet, in contrast to the well-developed understanding of collisional mountain belts, such as the Alps and Himalayas, the origin of less elevated (1–2 km) passive margin highlands is still unknown. The eastern Australian highlands are a prime example of these plateaus, but compared to others they have a well-documented episodic uplift history spanning 120 million years. We use a series of mantle convection models to show that the time-dependent interaction of plate motion with mantle downwellings and upwellings accounts for the broad pattern of margin uplift phases. Initial dynamic uplift of 400–600 m from 120–80 Ma was driven by the eastward motion of eastern Australia's margin away from the sinking eastern Gondwana slab, followed by tectonic quiescence to about 60 Ma in the south (Snowy Mountains). Renewed uplift of ∼700 m in the Snowy Mountains is propelled by the gradual motion of the margin over the edge of the large Pacific mantle upwelling. In contrast the northernmost portion of the highlands records continuous uplift from 120 Ma to present-day totalling about 800 m. The northern highlands experienced a continuous history of dynamic uplift, first due to the end of subduction to the east of Australia, then due to moving over a large passive mantle upwelling. In contrast, the southern highlands started interacting with the edge of the large Pacific mantle upwelling ∼40–50∼40–50 million years later, resulting in a two-phase uplift history. Our results are in agreement with published uplift models derived from river profiles and the Cretaceous sediment influx into the Ceduna sub-basin offshore southeast Australia, reflecting the fundamental link between dynamic uplift, fluvial erosion and depositional pulses in basins distal to passive margin highlands.