Depends on the purpose of the segregation and if it is discriminatory in any fashion. For example sex segregated sex education ie separate sex education classes for boys and girls has routinely been held constitutional so the short answer is most likely - yes.
Unless one is inferior to the other one, then probably yes. If you don't like the policy, complain to the school board. If you don't like their answer, run for school board in the next election.
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