Around thirty pupils aged between 13 and 15 at the Roger-Vailland school in Poncin, close to Lyon, decided to stage the protest.
The school's principal was not happy with their choice of outfit and asked them to take their skirts off.
"As a result of verbal assaults, of which some of these girls have been victims, they have been asked to change," said Sylvain Weisse, reported Le Figaro newspaper.
Girls who refused to get changed were sent home for the day.
"I was wearing a flowery skirt that stopped just above the knee," said one girl on radio station RTL.
"It wasn't provocative. It seems a bit absurd to tell us to take off our skirts because we can't work while wearing them."
"It's boys, men and the rest of society that need educating," said a mother of another girl.
Women's rights group Ni Putes Ni Soumises (Neither Whore nor Submissive) said they were unhappy with the school's decision.
"It's degrading," said the group's president, Asthma Guenifi. "This type of attitude encourages the view that provocation can come from a girl wearing a skirt."
The group organises a "Day of the Skirt" every year on November 25th to encourage women to show their femininity without fear or prejudice.
Last week, as reported in The Local, a parliamentary report said schoolgirls as young as eight were already wearing padded bras, high heels and taking make-up bags to school. Read more about the story here.