Neeleman, who owns 6 percent of the New York-based airline's shares, will stay on as the company's non-executive chairman, while Dave Barger, its current chief operating officer, takes over as CEO.
Neeleman, whose airline brought live TV and a renewed emphasis on customer service to the skies, called the move a "natural evolution" of the company's leadership structure.
"As chairman of the board of directors, I will focus on developing JetBlue's long-term vision and strategy," he said in a statement.
In February, JetBlue's image as a customer-friendly airline was tainted when a snowstorm left thousands of travelers stranded in planes and airports throughout the northeast. Despite the public-relations damage, Neeleman refused to resign over the incident. The company subsequently took out full-page ads apologizing to travelers and presenting a customer bill of rights.
Neeleman founded the airline in 1998, after creating WestJet, a low-cost Canadian airline, in the mid-1990s. Today JetBlue offers up to 575 daily flights to 52 cities. Costs are kept low by operating only one type jet, rather than the higher maintenance and repair expenses of a fleet of different jets. Neeleman, who keeps his own salary low, is known to travel aboard flights in order to gauge customer satisfaction with the airline.
In 2004, Inc. magazine named Neeleman one of the nation's 25 most fascinating entrepreneurs.