The company was considering leaving Queens when its lease at its current building ends in 2023.
The airline already operates a training center in Orlando and has a subsidiary based in Fort Lauderdale.
Instead, the airline said it will negotiate a new lease for its headquarters building.
CEO Robin Hayes said New York is still a great place to live, work and visit, and JetBlue wants to help the city recover from the pandemic.
JetBlue also has plans to expand its flagship terminal at JFK Airport and that will create thousands of new jobs.
Plans are also in the works for a whole new Terminal 6 at JFK that will connect to JetBlue's existing Terminal 5.
Once the plan is approved by the board, the Port Authority will finalize its lease agreement with the construction company for the nearly $4 billion project.
Groundbreaking is expected to happen next year with the first new gates opening in 2025.
"New York and JetBlue Airways have enjoyed a productive partnership that has actively promoted travel to all corners of New York, and we are pleased that JetBlue has committed to keep its headquarters in Long Island City, Queens, where they have operated for more than 20 years," Gov. Andrew Cuomo said. "This announcement, on the heels of the Port Authority plans for a new Terminal 6 at JFK Airport, is a testament to New York's position as a global hub for business and travel and a tremendous boon for the state's post-pandemic economic recovery..
The governor went on to say that revitalizing the travel and tourism industries is key to building back better, smarter and stronger.
(The Associated Press contributed to this report.)
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