The teenagers, who come from mainstream secular schools across Israel, say their teachers insist on the ban to protect them from unwanted male attention, despite recent temperatures of up to 45C (113F).
"Why does a woman have to suffer sexist and chauvinist comments just because it's hot?" one anonymous writer posted on Facebook.
"There's a situation here in which they are blaming the victim," a 14-year-old student said in remarks quoted by Haaretz newspaper.
"They tell the girls not to come in shorts because the boys stare. We are the victims and they're blaming us."
Girls who defy the ban say they have been barred from sitting exams, have had their cellphones confiscated and have had their parents called into school, the paper said.
Students involved in the shorts protest have even written a letter to the far-right Education Minister Naftali Bennett, Channel 2 television said.
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"Recently there have been many reports of cases where girls from all over the country were discriminated against in schools over a dress code which is different for boys and girls," the letter said.
"We are in an educational system that is supposed to be equal and so we are asking you to intervene in the matter and support the struggle for a unified school dress code for boys and girls and of course to enforce it without discrimination."
Bennett's office declined AFP's request for comment.
The protesters' Hebrew-language Facebook page, entitled "Teaching schools a lesson in equality", is calling for a demonstration outside the Israeli parliament on June 16.
This Wednesday, parliament is to debate an urgent motion on the subject submitted by lawmaker Michal Biran, of the opposition Zionist Union party, her office told AFP.
"We should ask ourselves what message we are giving to these young women: that they should be ashamed of their bodies?" an aide quoted her as saying.
"I expect the education minister to intervene and cancel this discriminatory ban. Such a ban only perpetuates the stigma that woman is an object."