A motion was defeated asking EMSB commissioner Sophie De Vito to step down following comments she made online that some people call "racist and anti-francophone".
The court ruled that several sections of the law cannot be applied to English school boards, including those that set limits on who can run for election and sit on the boards.
The action filed in Quebec Superior Court comes just over a week after several Muslim organizations also announced they were taking province to court over the prayer room ban.
Quebec's auditor general says more than one-quarter of teachers who worked in the province's classrooms during the 2020-21 school year weren't legally qualified.
Education Minister Bernard Drainville ordered the ban after reports of at least two Montreal-area schools permitting students to gather on school property for prayer.