The move, formally confirmed on Thursday, will allow French prosecutors to investigate her over tweets she sent in December 2015,
which showed images of killings by ISIS militants.
French law prohibits the distribution of violent images or incitement of terrorism.
Announcing the result of the vote on whether to lift the immunity, Parliamentary President Antonio Tajani said a “clear majority” of members backed the motion.
Le Pen declined to comment when contacted by CNN.
As an MEP, Le Pen, leader of the National Front, enjoys immunity which covers freedom of speech — but that immunity can be lifted if a request is made by the authorities of the person’s member state.
In this case, the request was made by a prosecutor in Nanterre, in the west of Paris.
Under French law, the maximum penalty for distributing violent images is three years in prison and a fine of up to €75,000 ($79,000).
The lifting of her immunity relates to this case only and any action is unlikely to occur before the first round of voting on April 23.
This is not the first time Le Pen’s immunity has been lifted by the EU Parliament, which also took a similar step in 2013.
That allowed her to be prosecuted in 2015 with “incitement to discrimination over people’s religious beliefs” after she compared Muslims praying in public to the Nazi occupation of France during the Second World War
. She was acquitted by the court in Lyon.
Le Pen is already under scrutiny over allegations that members of her staff were paid for non-existent jobs at the European Parliament.
Le Pen initially admitted they had been paid while not working, the European Anti-Fraud Office (OLAF) said. She later denied having said so.