The former American Idol winner gave her rendition of the track during a show at the Nokia Theatre on Tuesday evening (April 3), with footage uploaded to YouTube by an audience member.
Clarkson introduced the track by saying that she had received "so many requests" at a number of shows to cover a song by "the lovely Britney Spears".
"I'm expecting everyone - I know you know this song - on these 'ohs' (the chorus)," she said.
Clarkson closed her performance by admitting: "I love that song."
The show also included appearances from Michelle Branch, Reba McEntire and The Voice coach Blake Shelton, who stepped in for Jason Aldean on a rendition of his duet with Clarkson 'Don't You Wanna Stay'.
Clarkson and Aldean were honoured with two awards at Sunday night's ACMs in Las Vegas for the track.
Watch Kelly Clarkson and Blake Shelton singing together below: