Attorneys for the school district said the complaint would allow them to get more evidence in front of a judge.
RELATED: Fresno County orders Immanuel Schools to shut down after it brings kids back to campus
They said Fresno County has taken "arbitrary and capricious" actions to stop them from holding in-person instruction.
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The school opened its campus to students and staff in August in violation of the state emergency order and a county health officer order.
A hearing is set for next week on the county's request for an injunction.