"You can pass on my respects to the Grand Mufti, but I will not cover myself up," Le Pen told reporters.
The press office for the Grand Mufti said that Le Pen's aides had been informed beforehand of their requirement for her to wear a headscarf for the meeting.
France's Le Pen launches campaign with anti-EU message
Le Pen has been visiting Lebanon as she seeks to bolster her presidential credentials.
Opinion polls say Le Pen is likely to get the highest score in the first round of voting which is to be held in April but then lose to a mainstream candidate in the decisive second round vote in May.
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