Napolitano announced the vigilance campaign in Penn Station, the nation's busiest train station. The campaign is part of a national information-sharing partnership with Amtrak.
The slogan was inspired by the Metropolitan Transportation Authority's admonition to traditionally mind-your-own-business New Yorkers. Since 2002, posters encouraging, "If you see something, say something" have become a daily sight for New York subway riders.
The phrase took on additional power after the foiled Times Square bomb plot. On May 1, street vendors in Times Square noticed a smoking SUV with its blinkers on, engine running and no one inside. They decided to say something to a police officer.
Police were able to dismantle a crude but dangerous homemade bomb inside the SUV and clear the square. The vendors were hailed as heroes for taking action after seeing something suspicious.
Napolitano called "If you see something, say something" one of the most successful public efforts to date. She said security requires the public's cooperation.
"All play a critical role in increasing awareness and improving preparedness," she said.
Napolitano also swore in John Pistole as administrator of the Transportation Security Administration. He is a former deputy FBI director who was confirmed by the Senate last week to fill the top TSA job.
Pistole called "see something, say something" a way to promote an engaged and informed public.
Napolitano appeared two days after her office issued a threat assessment on mass transit and railroads.
The assessment, obtained by The Associated Press, said there are no known terrorist plots against mass transit in the U.S., but the systems are considered desireable targets because they are critical infrastructure.
The campaign also kicked off the same day the NYPD graduated a new class of 103 police officers who will be assigned to the city's transit bureaus.
Napolitano was spending the rest of the day on a train tour of the Northeast corridor, making stops in Newark, N.J., and Philadelphia to raise awareness about the campaign on her way back to Washington, D.C. The route is the busiest passenger rail line in the nation.
The Department of Homeland Security has spent more than $44 million since 2006 on safety awareness efforts. Out of that, $13 million went to the "see something, say something" campaign.
Napolitano isn't the first to want the six-word, alliterative phrase for her own. Transit authorities in Boston, Chicago, Amsterdam and about 50 other locations have received permission to use the trademarked slogan from New York's MTA.
Authorities say the power of the phrase is in its simplicity.
"It's right to the point," said MTA spokesman Kevin Ortiz. "It's engaged the public in serving as the eyes and ears of our system."
Amtrak travelers will see more security through July 6 for the holiday weekend. There will be more officers on trains, bomb-sniffing dogs, ID checks and random bag searches at unannounced locations.
Associated Press writers Colleen Long and Eileen Sullivan in Washington contributed to this report.