The new clock was launched Thursday. It's located at the institute's Boulder center.
The clock is the nation's civilian time standard. The U.S. Naval Observatory maintains military time.
The new clock, called NIST F-2, is about three times more accurate than the old one, called NIST F-1, the Boulder Daily Camera reported.
The institute plans to operate both for a while and use comparisons to improve them.
Banks, computer networks and others use the atomic clock to synchronize their own. The institute's radio broadcasts are used to update about 50 million timekeepers daily. Its Internet service gets about 8 billion automated synchronization requests a day.
"Nothing here is going to change the way we live tomorrow, in terms of having a three-times-more-accurate clock," said physicist Steven Jefferts, lead designer of the new clock. "But these technologies keep getting adopted for use in our society, so we have to keep inventing things to make them work better."
Both clocks use cesium atoms to determine the exact length of a second. They measure the frequency of a particular transition in the cesium atom - which is more than 9.1 billion vibrations per second - and use it to define one second.
One key difference is that the old clock operates at about 80 degrees Fahrenheit (26.6 Celsius) while the atoms in the new clock are kept at about minus 316 degrees Fahrenheit (minus 193 Celsius). That cooling significantly lowers the background radiation and reduces some tiny measurement errors in the old clock.