Fresno County's injunction case is still set for a local judge to hear next week, but county leaders anticipated he would follow the lead of the California Supreme court.
The county also served an inspection warrant at Immanuel Schools on Wednesday.
The school opened its campus to students and staff in August in violation of the state emergency order and a county health officer order.
Attorneys for Immanuel Schools, Robert Tyler and Jennifer Bursch, released the following statements:
"This court entry has no effect of law. It simply means that we will have to start the litigation by filing our claims in the superior courts because the court is not willing to permit this case to skip the lower courts. Once we proceed through the normal process, we believe we will still be victorious in the end. No public or elected official should have the authority to have unbridled discretion to deny children their fundamental right to equal protection and access to equal education," said Robert Tyler.
"The Court's denial of our petition for review is disappointing and while we have not yet exactly decided our next move, be assured we are prepared to continue fighting for the rights of the vulnerable children of California," said Jennifer Bursch.