Jan Mayen is a small volcanic island situated in the Norwegian–Greenland Sea. The entire island was covered by a contiguous ice cap during the Last Glacial Maximum. The deglaciation of the ice cap was interrupted by a glacier advance in the southern part of the island in the Early Holocene. Today, there are no glaciers in this area, and until now it has been unknown whether any glaciers survived there into the Middle–Late Holocene. We show here that glaciers existed at several sites in the mountain areas of southern Jan Mayen. The investigations were triggered by the discovery of a relict glacier completely covered by tephra and impacted by a lava flow. Samples of ice from the glacier have 18O values that are isotopically indistinguishable from modern precipitation values and fall along the local meteoric water line trend. The lava flow in the glacier catchment and sculpted forms along the base of dry meltwater channels in bedrock show that glacier melting was abrupt and marked by sudden meltwater outbursts (jökulhlaups). Three more sites in southern Jan Mayen have meltwater channels with sculpted beds, gorges and/or sediments associated with lava flows and can be attributed to jökulhlaups caused by rapidly melting glaciers. Radiocarbon dates associated with glacial outwash sediments, cosmogenic dates of meltwater channel incisions, and cosmogenic and K‐Ar dates of lava flows associated with former periods of rapid glacier melting show that the four glaciers collapsed at different times in the Holocene. None of the glaciers reformed after their collapses despite subsequent cooling event(s). Likely, the glaciers were on the brink of existence before their sudden demise.