The low-fare airline on Thursday appointed Chief Operating Officer Dave Barger as its new chief executive, effective immediately. Neeleman had been chief executive since 1998 and will retain his role as chairman.
The move comes after storms on Valentine's Day and St. Patrick's Day essentially shut JetBlue down, forcing the cancellation of nearly 1,700 flights and stranding thousands of travelers throughout the Northeast.
To prevent a recurrence, JetBlue drafted a "customer bill of rights," the gist of which is that the company now issues vouchers to some customers who experience delays.
The canceled flights and vouchers cost JetBlue $41 million, contributing to the company's first quarter loss of $22 million, or 12 cents a share. That was an improvement over the year-ago quarter, but was less than analysts had originally expected.
Last month, JetBlue lowered expectations for the rest of the year.
In a statement, Neeleman characterized the change as "a natural evolution" of JetBlue's leadership structure.
Barger, 49, will retain his role as president. He joined JetBlue as president and chief operating officer shortly after Neeleman founded the airline in 1998.
Shares of the airline, which operates more than 575 flights daily to 52 destinations, jumped 54 cents, or 5.1 percent, to $10.94 in morning trading. The stock is off 35 percent since mid-January, when it hit an intraday high of $17.02.