Understanding changes in intraseasonal rainfall variability is critical for improving sub-seasonal prediction. While the amplification of intraseasonal rainfall variability across Australia has been reported, the spatial heterogeneity of this intensification has been overlooked. Here, we observe that the intraseasonal rainfall variability has been intensified particularly over northeastern Australia during the wet season (November–April) over the past four decades. The intensified intraseasonal rainfall variability is primarily attributed to enhanced intensity of precipitation events, rather than drier spells. Moisture budget analysis indicates that the intensification of intraseasonal abnormal rainfall events over northeastern Australia is primarily due to the strengthened vertical advection of background moisture caused by the intraseasonal vertical motion anomalies. In this process, the strengthening of intraseasonal vertical velocity driven by changes in intraseasonal wind convergence plays a dominant role, accounting for over 90%, whereas the effect of background moisture changes is relatively less significant. Our findings highlight northeastern Australia as a hotspot for amplified intraseasonal rainfall variability, rather than the whole of Australia. This study provides fundamental insights into northern Australia's changing climate, and highlights the important role of intraseasonal circulation on northeastern Australia rainfall variability.