Jany is being replaced by Stephan Lynen, a 49-year-old who currently heads the Muttenz-based chemicals maker's additives business unit after joining Clariant in 1998 as an internal auditor.
Jany is leaving for the CFO job at Maersk, whose $39 billion in annual revenue will be nearly 10 times that of Clariant after the Swiss company completes a shrinking exercise following the disposal of units that account for a third of its sales.
Lynen arrives as the Swiss company is still trying to find a CEO in the wake of the sudden departure of Ernesto Occhiello amid the collapse of a planned joint venture with Clariant's biggest shareholder, Saudi Basic Industries.
"We very much regret Patrick Jany's decision to leave Clariant," said Chairman Hariolf Kottmann, who is filling the CEO role on an interim basis. "Patrick Jany has been with our company for 25 years and has played a major role in our success story."
Kottman said Lynen's 22-year career at Clariant gave him the "perfect profile" to replace Jany.
Maersk has also seen turmoil at the top, with the departure of its CFO last November to join General Electric, just after the shipper's chief operating officer exited to join Swiss headquartered rival Mediterranean Shipping Co.
(Reporting by John Miller, editing by Riham Alkousaa and Brenna Hughes Neghaiwi)