The J/P Health Relief Organization will include five Haitians on the nation's team for the 26-mile run.
The two-time Oscar-winning actor made comments about the sponsorship at the world premiere of his film "The Secret Life of Walter Mitty" at the New York Film Festival.
"It's rewarding. I just came back from Port-au-Prince, where I visited our Haitian marathon runners, and to see that great discipline that Haitians have and that great spirit and the excitement that they have visiting New York for the first time."
The 53-year-old actor stars in "The Secret Life of Walter Mitty" alongside writer-director Ben Stiller.
Penn started the organization after a catastrophic magnitude-7.0 earthquake ripped through Haiti in 2010, killing more than 100,000 people.
The New York City Marathon takes place on Nov. 3.
The Associated Press contributed to this report.