The case of the school student, identified as Sarah K by the Ardennes regional newspaper, has stirred up a Twitter storm with the hashtag #JePorteMaJupeCommeJeVeux (I wear my skirt as I please) trending and facetious remarks about skirt length and secularism being swapped.
One Tweet sported a photo of far-right leader Marine Le Pen in a flowing dress, speculating that she had converted to Islam.
Regional education officials insisted on Wednesday that Sarah K had not been expelled from school but confirmed that she had been asked to come back to school in "neutral clothing".
Her father had not wanted her too comply, they said.
Sarah was prevented from attending classes on the 16 and 25 April, according to Ardennes, which said her parents were "furious" about the ruling.
She wears a hijab headscarf in her free time but has been taking it off when she arrived at school.
But when she arrived in a skirt judged "too long", her headteacher, Maryse Dubois, claimed it broke France's 2004 law banning "ostentatious signs" of religion in schools.
"It is sometimes difficult to distinguish simply what is wearing an ostentatious religious symbol, provocation or the temptation to test the limits of the rules," the local education authority said in a statement. “When it comes to concerted protest actions by students, which follow other more visible incidents linked for instance to wearing the veil, the secular framework for education must be firmly reminded and guaranteed."
"This skirt is really nothing special," Sarah commented. "It is quite simple. It is not ostentatious. There is no religious symbol at all."
Anti-Islamophobia campaign Le Collectif contre l'Islamophobie en France (CCIF) says that 130 students were prevented from attending classes in French schools due to the secular law during 2014 and claims that the majority of discrimination against Muslims take place in state-run institutions.