The name Aysen may come from the Huilliche word "Achen," meaning "to crumble". Another theory suggests that it was a term used by the Chonos culture meaning "going more to the interior," in reference to the Fjord of Aysen that stretches east from the Moraleda strait.
During the 1990s, it was suggested that the name might be derived from an 1831 map made by captain Robert Fitz-Roy, who made an expedition to the coast onboard the Beagle with Charles Darwin and labeled the area around modern Aysen province with the words "Ice End." This theory, however, was largely dismissed because the name "Aysen" appears in documents of the explorer Father Garcia, who make an expedition to this region in 1766, more than 60 years prior to the arrival of the Beagle. Despite this, the Fitz-Roy myth has become popular among the many European tourists who visit Patagonia each year.