"We want to thank Jeff for his six months at the company and wish him all the best," the statement released late Sunday read.
Jones was named Uber's President at the end of August. He previously ran marketing for Target.
Jones headed Uber's ride-hailing operations, marketing and customer support, and was second in command to CEO Travis Kalanick.
The company, valued at $68 billion, has had a rocky few months, the CNN report said.
In a letter to employees on Sunday, Kalanick said that Jones made the decision after the company said it would hire a chief operating officer.
Kalanick is looking for a new second in command who could help him steer the company's trajectory.
"Jeff came to the tough decision that he doesn't see his future at Uber," Kalanick wrote.
Jones did not immediately respond to a request for comment, CNN said.
Uber has already lost several big executives since February. Uber's head of growth and product, Ed Baker, resigned from the company in March.
Amit Singhal, its head of engineering, resigned in late February after it was reported that he had left a previous job at Google because of sexual harassment claims.