(CNN) Students returning to school this fall are likely to face some confusion as school boards struggle with the issue of access to bathrooms for transgender individuals.

A year-and-a-half after the Supreme Court cleared the way for same-sex marriage nationwide, there is a new frontier for LGBT litigation and it concerns transgender rights.

The legal battle is playing out in some school districts, led by a transgender male student in Virginia who seeks to use the bathroom that corresponds with his gender identity, as well as in courts across the country, most notably in North Carolina where the Justice Department has filed a federal civil rights lawsuit against the state's 2013 bathroom law.

Last April, a federal appeals court ruled in favor of Virginia resident Gavin Grimm, who fought the school board's new policy at Gloucester High School that denied him access to the boys' bathroom but allowed him the use of recently constructed single-stall unisex restrooms.

"Forcing a transgender student to use separate restrooms from everyone else interferes with that student's equal access to the resources and educational opportunities of school," ACLU attorney Joshua A. Block, Grimm's lawyer, had argued in court papers.

But lawyers for the school board won an emergency bid from the Supreme Court to temporarily freeze the opinion pending appeal. On Monday, they will ask the justices to take up the case this term.

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For now, Grimm will return to school this fall unable to use the boys' bathroom.

Grimm's case had a ripple effect on other schools.

Last June, for example, Charlotte-Mecklenburg School District in North Carolina had put forward regulations directing that transgender students could use the bathroom of their gender identity.

But after the Supreme Court issued a temporary stay in Grimm's case, the school district changed course.

Superintendent Ann Clark released a statement saying that while the school district "remains committed to nurturing a safe and welcoming learning environment for every student" the district was putting a "temporary hold" on the regulation.

The Obama administration has thrown its weight behind transgender students.

"We see you," Attorney General Loretta Lynch told transgender individuals when she announced the lawsuit in May. "No matter how isolated or scared you may feel," she said, "the Department of Justice and the entire Obama administration wants you to know that we see you."

Lynch's words came as welcome relief to those who believe that LGBT opponents, having lost at the Supreme Court on same-sex marriage, are now targeting the transgender community.

In May, the departments of Justice and Education told public school districts and colleges that receive federal funding that it interprets "sex discrimination" under Title IX, a federal law that bans sex discrimination in schools, to include claims based on gender identity.

"A school may not require transgender students to use facilities inconsistent with their gender identity," the guidance reads.

The administration's guidance outraged Texas Attorney General Ken Paxton who led a charge on behalf of several states and last week won a nationwide injunction from a district court judge in Texas barring federal agencies from taking action against the schools that disagreed with the guidance.

Related: Judge Temporarily Blocks Obama School Transgender Bathroom Policy

That injunction came down late on a Sunday night, the night before many students were returning to school.

Paxton praised the ruling saying in a statement that the President was "threatening to take away federal funding from schools to force them to conform." States and school districts "are charged under state law to establish a safe and disciplined environment conducive to student learning," he added.

The Justice Department said it is reviewing options on how to respond. 

On Thursday, Paxton went a step further and advised educational institutions in Texas that they "need not change their policies regarding intimate facilities to comply with the unenforceable federal guidelines, so long as this injunction remains in place."

Dru Levasseur, director of the Transgender Rights Project at Lambda Legal, blasted the district court's ruling, saying it would cause confusion.

He stressed that while the injunction prevents federal agencies from revoking federal financial assistance from schools who don't agree that Title IX protects claims of gender identity discrimination, the judge did not rule on whether transgender students could use the restroom of their gender identity.

Levasseur says that for years transgender students have been using the restroom according to their gender identity, but now "opponents are preying on the lack of understanding of who transgender people are, and they are bringing baseless challenges."

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Legislation has been introduced in 15 states that could negatively impact transgender individuals, according the Williams Institute at the University of California School of Law. The group estimates that nearly 300,000 transgender adults and youth (ages 13 and above) reside in those states.

But Matt Sharp, a lawyer for the Alliance Defending Freedom, says the Obama guidance represents an overreach of federal authority into an area that properly belongs to state and local school districts. His group represents students, parents and a school boards in Ohio and Illinois who are suing the federal government over its interpretation of Title IX.

He argues that schools are trying to accommodate transgender youth by offering options such as single stall restrooms and changing rooms.

"The schools have found the right balance to protect everyone's privacy rights while at the same time showing compassion for those struggling with gender identity issues," said Sharp.

"The government is exceeding its power in telling the school boards that they violate Title IX for simply maintaining separate locker rooms and restrooms for boys and girls based on their biological sex, something schools have been doing for decades," Sharp added. "If there is confusion this fall, it is the fault of the Obama administration."