The flight was one of four hijacked by al-Qaeda terrorists, but the only one that failed to meet its intended target, believed to be the White House or the U.S. Capitol.
The passengers attempted to regain control of Flight 93, and the Boeing 757 crashed in a field near Shanksville, Pennsylvania. All aboard were killed.
The public is invited to participate in the Portola Valley event, which starts at 9 a.m. at Triangle Park, at the corner of Portola and Alpine roads.
In the past, 75 to 100 people have participated, including kids on bikes, parents with strollers, and "last year we even had a girl on horseback," says Dorothy Garcia Bachler, who was Andy Garcia's wife at the time of his death.
After the run is a pancake breakfast, and firefighters will be cooking.
"As you know, the firefighters played a huge part in the events in New York, the Pentagon as well as Shanksville," Ms. Bachler said in a statement. "The firefighters have been especially important to me and my family through the years."
She gives special thanks to Kevin Bianchiani for his "continued support and generosity for our event."
There will be a time of silence and reflection as the names of those aboard Flight 93 are read.
"My granddaughter, Bella Bachler, will be singing an American favorite," Ms. Bachler said. "It is my sincere hope that we will never forget the heroism of our loved ones as we give honor to those who gave their lives for us."