Understanding the timings of interhemispheric climate changes during the Holocene, along with their causes, remains a major problem of climate science. Here, we present a high-resolution ¹⁰Be chronology of glacier fluctuations in New Zealand’s Southern Alps over the past 7000 years, including at least five events during the last millennium. The extents of glacier advances decreased from the middle to the late Holocene, in contrast with the Northern Hemisphere pattern. Several glacier advances occurred in New Zealand during classic northern warm periods. These findings point to the importance of regional driving and/or amplifying mechanisms. We suggest that atmospheric circulation changes in the southwest Pacific were one important factor in forcing high-frequency Holocene glacier fluctuations in New Zealand.