The latest expulsions brought to five the total number of girls so far expelled under the new "secularity law", which has drawn complaints from some Muslim groups that it represents a form of discrimination against Islam.
Under the new legislation, students have been barred from sporting religious conspicuous insignias such as the Muslim hijab, the Christian cross and the Sikh turban in state schools.
The headmaster of Louis-Armand school in the eastern city of Mulhouse, Rodolphe Echard announced the expulsion of one girl, identified as Manele, who had returned to classes after the summer break wearing first a headscarf and later a bandana.
In another case in Mulhouse, a girl identified as Tuba was expelled from the Lavoisier school.
Another girl was also barred from the Jean Guehenno school in the northern town of Caen on Wednesday.
On Tuesday, two teenage Muslim schoolgirls were expelled from another school in Mulhouse, the first such actions to be taken under the new law.
Under the legislation that came into force in September, the school authorities must first try to persuade girls to remove the headscarf and only if they persist in refusing can they be expelled.
The students can appeal the decision.
There are at present 72 school students within the state school system in France who are currently breaking the new law, according to education ministry figures.