Company veteran Clerc, who currently heads the company's Ocean & Logistics business, is taking the helm at a time of slowing demand for transport and logistics as a global recession looms.
"The strong tail winds that benefited the supply chain industries during the pandemic are coming to an end," said chair of the board Robert Maersk Uggla in a statement.
"With an increasingly challenging outlook, the board believes Vincent holds the right experience and capabilities as CEO to pursue and oversee Maersk's strategic and organisational development in the years to come," he added.
Clerc, a Swiss citizen born in 1972, joined Maersk in 1997 and has since held several senior positions including chief trade and marketing officer and chief commercial officer.
He has been pivotal in the firm's expansion beyond its core ocean freight business.
Biggest Shipping And Logistics Company
Copenhagen-based Maersk is one of the world's biggest shipping and logistics companies, handling supply chain logistics for large customers like Walmart and Nike.
It employs more than 100,000 people in 130 countries.
Skou, who has been in the job since 2016, oversaw the group's transformation from a conglomerate into an integrated logistics company.