The airline is also offering a fee waiver for customers traveling to or from Orlando who need to make last-minute travel changes.
In a statement, the airline said it wants to "do our part to help the victims of this tragedy, as well as support the Orlando community through this difficult time."
"This weekend’s events are felt by all of our 19,000 crewmembers, many of whom live in, work from and travel through Orlando – one of our focus cities – at Orlando International Airport, our Orlando Support Center and JetBlue University," the company's website states.
The airline says it will also make a charitable contribution to help support the victims and their families.
The airline is just one of many organizations that have teamed up to help support those affected by the violence at Orlando's Pulse nightclub. The shooting, carried out by a lone gunman, was the deadliest in the nation's history.
Find out how to help Orlando here, or donate below.