Le Pen lost parliamentary immunity last March, which cleared the way for authorities to prosecute her over the tweets she posted in 2015.
The charges were issued for "distribution of violent images", reports the Associated Press. If the case goes to trial and she is convicted of the offense, she could face up to three years in prison and a fine of €75,000 (about $91,390).
The images, tweeted with the caption "This is Daesh", included a picture of the decapitated body of USA reporter James Foley, a man in an orange jumpsuit on fire in a cage, and another man being driven over by a tank.
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However, as a member of the French parliament, Le Pen had some immunity against prosecution.
The judge's decision to step up the investigation comes a little over a week ahead of the National Front's annual congress, where Le Pen is expected to lay out her plans for rebuilding the party after it's loss to President Emmanuel Macron's La République En Marche! in last year's election. She posted them in the wake of the November 2015 IS attacks on Paris, as she accused the government of not doing enough to protect France.
"If they are trying to silence me, they will not succeed", she said in another interview.
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The others showed a man in an orange jumpsuit being driven over by a tank and a man being burned alive in a cage. Ms Le Pen later deleted the photograph, claiming she did not know it was Mr Foley.
Manuel Valls, France's Prime Minister at the time, described the photos as "monstrous", adding that Ms Le Pen had shown "political and moral failing" and her "non-respect for victims".
"I am being charged for having condemned the horrors of Daesh", Le Pen told the news agency AFP.
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It's one of multiple legal cases targeting Le Pen or the National Front. The party could also end the honorary presidency of Le Pen's father and National Front founder Jean-Marie Le Pen, as part of a protracted family feud.