The festival, which was created to help lower Manhattan recover economically from the attacks, begins April 25 and runs through May 7.
"United 93" chronicles in real time the hijacked United Airlines flight, which passengers tried to retake before it crashed into a field outside Shanksville, Pa.
Paul Greengrass ("Bloody Sunday," "The Bourne Supremacy") wrote and directed the Universal Pictures movie, which is scheduled to open in theaters April 28.
The victims' survivors, as well as members of other Sept. 11-related groups, will have a chance to see the film ahead of time at the premiere.
"9/11 changed us, in indescribable personal ways, but also by forever altering our downtown community," festival co-founder Jane Rosenthal said Wednesday in announcing the selection. "As we enter our fifth festival, we are honored to showcase a film that portrays a story of bravery and sacrifice of the men and women who dedicated their lives that day aboard United Flight 93. We are humbled to host their families, first responders, and others who were most profoundly affected that day."
A made-for-TV movie about the hijacking, "Flight 93," was the most-watched program ever on A&E when it aired two months ago, drawing 5.9 million viewers.