The timing and controls of interhemispheric Holocene climate change have remained poorly understood, primarily because of the absence of well-dated and continuous climatic records in terrestrial environments. Here we report a new probability-based meta-analysis of 1185 14C dates from fluvial sedimentary sequences in New Zealand and the UK, which provides a robust means of identifying centennial- and multicentennial-length episodes of Holocene river flooding. Statistical analysis shows that prior to large-scale human impact, which began at ca. 1000 cal. yr B.P., the incidence of extreme floods in New Zealand and the UK has been largely asynchronous during the Holocene. Major periods of flooding are controlled by large-scale shifts in atmospheric circulation, which alter the frequency of extreme precipitation events. Our novel synthesis demonstrates that short-term climate change, of sufficient magnitude to modify flooding regimes, was out of phase in the temperate maritime regions of the Northern and Southern Hemispheres during much of the Holocene. This supports recent evidence from both glacial and marine records that Holocene climate changes may have been antiphased between the polar regions and that this could have been related to variation in the strength of deep water formation.