Le Pen was charged with "dissemination of images of a violent nature that could be seen by minors" by a judge in Nanterre, near Paris, on Thursday, sources said.
The offence carries a maximum sentence of three years in prison and a 75,000-euro fine.
The National Assembly, where she sits as an MP, lifted her parliamentary immunity in November, as had the European parliament in March last year.
"I'm ashamed of the image we're presenting to the world," Le Pen told the LCI TV channel. "When you attack Daesh [IS] you're charged. If they're trying to shut me up, they won't succeed."
Le Pen and far-right MP Gilbert Collard addressed the tweets in 2015 to journalist Jean-Jacques Bourdin, whom she accused of drawing parallels between the FN and IS during an interview.
Under the message "This is Daesh", they showed graphic pictures of IS violence, including the decapitated body of American journalist James Foley, someone being driven over by a tank and a man on fire in a cage.
Foley was captured in Syria in 2012 and beheaded in 2014. His parents have accused Le Pen of posting “shamelessly uncensored” images for political gain.
National Front faces other charges
Le Pen has over two million Twitter followers, although she had fewer at the time of the tweets.
Collard was charged with the same offence several weeks ago.
She scored a record vote for the far-right party in last year's presidential election but failed to live up to expectations after a TV debate wth the eventual winner, Emmanuel Macron, where her performance was widely judged to be disastrous.
Her party faces a number of legal investigations, notably over allegations of fake jobs in the European parliament.