The girl, named as Sarah, was twice blocked from classes because the principal said her skirt broke a ban on religious signs in schools.
The girl removed her headscarf but said the skirt was not a religious symbol.
The case has provoked angry reactions online.
The hashtag #JePorteMaJupeCommeJeVeux (I wear my skirt how I want to) has had more than 45,000 tweets since April 28.
Sarah was sent home in Charleville-Mezieres in the northern Champagne-Ardenne region twice in April, according to reports.
Nicolas Cadene, an official advising the prime minister on secular issues, has said that wearing a long black skirt to school does not break the rules.
A ban on Muslim headscarves and other “conspicuous” religious symbols at state schools was introduced in 2004, and widely welcomed in a country where the separation of state and religion is enshrined in law.
However, critics say some schools are increasingly imposing extreme interpretations of the ban.
Eight Muslim students were told to change by their school in Montpellier when they arrived in long skirts last month, local media say.
The Collective Against Islamophobia in France (CCIF) said they had recorded nearly 130 similar incidents in the country last year.
In 2011, France became the first European country to ban the full-face Islamic veil – the niqab – in public places.
Most of the population – including most Muslims – agree with the government when it describes the face-covering veil as an affront to society’s values. Critics – many outside France – say it is a violation of individual liberties.
The European Court of Human Rights upheld the ban in July 2014 after it was challenged by a 24-year-old French woman, who argued that it violated her freedom of religion and expression.
France has about 5 million Muslims – the largest Muslim minority in Western Europe – but it is thought only about 2,000 women wear full veils.
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