Jacob Aarup-Andersen will replace Cees 't Hart, who said earlier this month he would retire at the end of September.
The exact starting date of Carlsberg's new CEO would be announced later, the world's third largest brewer said in a statement.
Aarup-Andersen became CEO at ISS in 2020 after he had been rejected by Denmark's financial regulator to take over the helm at Danske Bank, on the grounds that his banking experience was not sufficient.
During Aarup-Andersen's tenure of more than two years at ISS, shares have risen around 50%.
Carlsberg's executive team has undergone large changes in the last year, with former chair Flemming Besenbacher retiring in March and ex-chief financial officer Heine Dalsgaard leaving the company in December.
'Innovation Or Agility'
While Aarup-Andersen does not have a background in the beer or food industry, his appointment could bring some sought-after "innovation or agility" to Carlsberg, Nordnet analyst Per Hansen told Reuters.
"Carlsberg has probably said: We are forced to compromise with industry knowledge, in return we get someone who is very strong in the financial disciplines," Hansen said.
Commenting on the appointment, chair of Carlsberg's supervisory board, Henrik Poulsen said, "Jacob brings a unique blend of excellent strategic skills, financial acumen and discipline, global operational experience and an engaging and purpose-led leadership style.
"We’re pleased that he'll be leading the next stage of Carlsberg’s value-creating growth journey, and we’re looking forward to welcoming him at Carlsberg."