The drill gave various law enforcement agencies a chance to work together on security procedures on the rail system.
"I did notice some extra dogs and extra security," said commuter Courtney Mazzola, of Colts Neck.
The NYPD, Amtrak police and law enforcement from several agencies patrolled the trains, the stations and subways.
Those areas are highly populated and, therefore, a target, experts say.
Operation Rail Safe was a 4 1/2 hour drill that was intended to reinforce security cooperation on rail systems.
The practice run factored in lessons learned from the attacks in London and Moscow in recent years.
Security was evident inside and outside Penn Station and Grand Central Friday morning, and riders said they were thankful for it.
"I think that's great, if it helps keep the trains safe, then that's great," Long Island resident Stuart Barnett said.
Operation Rail Safe comes right on the heels of the state department's terror alert for Americans traveling in or to Britain, France and Germany.
It's just a coincidence that Operation Rail Safe happened the very same week, but as some riders pointed out, these coincidences are less surprising these days.
"You know, things have changed since 9/11, and you have to face the facts," said Andrea, a commuter from New Jersey.
Operation Rail Safe took place during the morning and evening commutes. The drill took place in major cities across the country.