"Dave Lowman and I have decided he will leave the firm," Frank Bisignano, the bank's chief administrative officer, said in a memo that was sent to bank staff on Tuesday.
A copy of the memo was obtained by Reuters.
"He worked here during extraordinary times and has said he will take some much needed time off," the memo said.
Lowman had joined JPMorgan from Citigroup in 2006. During his tenure at JPMorgan, the bank picked up bad mortgage assets through its acquisitions of investment bank Bear Stearns & Co and retail bank Washington Mutual.
JPMorgan Chief Executive Jamie Dimon in February sent Bisignano, a top aide, to the company's retail banking division to fix its struggling mortgage business.
(Reporting by David Henry, editing by Maureen Bavdek)