Thousands participated in the event, which retraces Siller's final footsteps from the Hugh L. Carey Tunnel, formerly called the Battery Tunnel, to the World Trade Center.
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This year, organizers are also honoring some U.S. service members.
Runners began in Brooklyn and ended on West and Murray streets across from the World Trade Center, the route Siller took when he abandoned his truck and ran through the tunnel towards the towers.
The event is a tribute to the 343 firefighters and first responders who were killed on 9/11, as well as the service members who died during the war on terror.
"First you feel hot, because that tunnel has no breathing," participant Scott Nokes said. "But then when you come out, and there's 343-plus flags, 343-plus firemen and police officers holding pictures of their brothers and sisters that were lost that day. You get past that, and you just feel it like I can't say you feel it."
At the starting line, firefighters, families, and city leaders waited for the airhorn to blow to go on a special journey, one that's personal for many runners.
"This event is important to my family, something that I like to run and remember the sacrifice 21 years ago," runner Kai Youngren said.
For first time runners like Tiffany Eckert, her family has benefitted from the foundation. She ran in memory of her late husband who died while fighting in the military over seas.
"I couldn't sleep last night," she said. "And every time I think about walking through the tunnel, I get choked up thinking about Stephen's story and my husband."
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Unlike previous years, the event will also pay a special tribute to the 13 service members lost last year during the U.S. withdrawal from Afghanistan.
Firefighters also came from as far as London and France just for the event.
Proceeds benefit the Stephen Siller Tunnel to Towers Foundation, supporting first responders and wounded veterans of the Iraq and Afghanistan wars.
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Siller's brother Frank set up the foundation, which has raised and spent hundreds of millions of dollars helping those affected by 9/11.
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