Angela Ahrendts, the former high fashion manager of Burberry, is invited to revive Apple's stores, going down after five years.
Apple said that Mrs Ahrendts will leave the company in April "for new personal and professional pursuits".
She is one of her highest paid executives, earning almost twice as much as boss Tim Cook in 2017.
Ms Ahrendts will be replaced by Deirdre O & # 39; Brien, whose role as Vice President of People will expand to cover retail.
During her time at Apple, Ms Ahrend's opened a number of flagship stores with the aim of creating a "community" as opposed to simply selling the company's latest product.
Cook said, "She has been a positive transforming force for both Apple's stores and the communities they serve. We all want her the very best as she begins a new chapter."
Ms Ahrendts was formerly CEO of Burberry, where she oversees her transformation from a British brand known for her controlled raincoats to a leading name on the world's catwalks.
When she left in 2014, she was one of FTSE 100's highest paid CEOs.
In 2017, Ms Ahrendts received $ 24.2 million. Compared to Mr Cook who took home 12.8 million.
Apple recently reported a sharp drop in revenue from its iPhone and suggested it could lower prices to boost demand.
Overall, revenue in the first quarter decreased by 5% to DKK 84.3 billion. USD compared to the same period last year.
Analysts at Wedbush Securities said the first reaction to Ms Ahrend's departure was surprising "when she was one of Apple's key leaders and a linchpin around running 500 plus stores on five continents and potentially seen by some as one future heir to Cook as CEO further down the line ".
But it said because Apple is entering a critical period of weak demand for the iPhone. Mrs. O & # 39; Briens 30 years working for the company is positive. "As an outsider that runs retail, it goes into one of the most crucial, defining periods for Cook & Co in its history would have been a risky effort."