As Melissa Baize drove her 10-year-old son to his first day of fifth grade Monday, her mind raced with a flurry of concerns familiar to any parent whose child has ever started at a new school.

“I hope he makes new friends. I hope he’s not too shy. I hope he sits with someone at lunch,” she told NBC News after dropping Trevor off at the Fort Worth Academy of Fine Arts in Texas.

But there was another concern that only a few parents would recognize: “I hope he’ll be able to use the boys’ bathroom.”

Trevor, a transgender boy, has a supportive family and a talent for drawing promising enough to land him a spot at a public arts charter school in Fort Worth. He received official permission from his new principal just last week to use the boys’ bathroom in accordance with his gender identity — a novelty for the aspiring artist, who is currently fond of drawing animals.

Trevor came out as transgender a year ago, and had to use the teacher’s bathroom at his last school. It wasn’t great, he said; but at least it was better than having to use the girls’ bathroom.

But hours before his first day, Trevor and hundreds of thousands of transgender students like him were dealt a devastating blow: Late Sunday, a federal judge granted a preliminary injunction blocking the Obama administration from enforcing new guidelines intended to allow students to use the bathroom and locker room matching their gender identities.

The 38-page order, issued by U.S. District Judge Reed O'Connor, came in response to a federal lawsuit filed last spring by 13 states against the Obama administration after it informed public school officials across the country that a failure to allow transgender students access to bathrooms consistent with their gender identities could result in a loss of Title IX funds.

The Department of Education had already stipulated two years ago that Title IX of the 1972 Education Amendments, which prohibits sex discrimination in federally funded education programs and activities, bars discrimination on the basis of gender identity as well. But the new guidance was arguably the Obama administration’s strongest action to date on behalf of transgender students.

While legal experts and LGBT advocacy groups were quick to point out that O’Connor’s ruling did not require schools to change their trans-inclusive policies or preclude transgender students from filing lawsuits on the basis of Title IX, some were still nervous the decision could have negative ramifications for the new school year.

“I think it might embolden districts with discriminatory policies to stand behind their decision to discriminate against trans students,” said Paul Castillo, staff attorney at the pro-LGBT group, Lambda Legal. “Meanwhile, trans students themselves are going to continue to suffer harm and different treatment in access to programs and activities, including access to facilities consistent with their gender identity.”

It’s a fear shared by nearly a dozen transgender students and their parents interviewed by NBC News.

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“My school district has been really good about giving me spaces and accommodations so I can feel safe in school, but a much bigger state power is working against me,” said 15-year-old Emme Goldman, a transgender girl whose home state of Wisconsin is part of the coalition suing the Obama administration. “It seems pretty scary … I have accommodations now, but will I have them in a couples months?”

“I'm scared for my son and for all youth who live outside of the gender boxes,” said one parent of an 11-year-old transgender boy in Missouri, where lawmakers earlier this year introduced a handful of bills that would ban students from using facilities matching their gender identities. “If the law changes here, my child would no longer be safe and we would have to find a plan B.”

Over the past three decades, there have been numerous court decisions that have found discrimination against transgender people to be a form of sex discrimination, which is already prohibited under several federal laws — including Title IX, Title VII of the 1964 Civil Rights Act, the 1974 Equal Credit Opportunity Act, the 1994 Violence Against Women Act, and the 14th Amendment’s Equal Protection Clause. Still, no federal law exists that explicitly bars discrimination on the basis of gender identity. A majority of states lack that official protection as well.

In April, the 4th Circuit Court of Appeals ruled in favor of a transgender teenager who had sued his Virginia school board for the right to use the boys’ bathroom in accordance with his gender identity. It was the first time a federal appeals court had weighed in on the so-called “bathroom issue,” one that has fast become a major fault line in the LGBT equality debate. But weeks before that student was set to begin his senior year, the nation’s highest court stepped in and temporarily blocked the lower court's ruling from taking effect.

Given the current makeup of the Supreme Court, which is still missing a ninth justice six months after the death of Antonin Scalia and the intense political standoff that followed, it is somewhat unlikely that the high court would take up the Virginia case this term. And, if and when the justices do decide to refuse the case, the 4th Circuit’s existing decision would take effect, allowing the student in question to use the boys’ bathroom for the remainder of his high school career.

Yet however likely that scenario may seem, the justices’ action earlier this summer marked an undeniable disappointment for LGBT rights advocates — one made all the more acute when paired with Judge O’Connor’s decision in Texas on Sunday.

“I initially was sick to my stomach,” said Hillary Whittington of O’Connor’s ruling. Her eight-year-old son, Ryland, currently enjoys protections in California that most transgender students don’t have access to. Still, the events of this summer made Whittington uneasy.

“I feel it’s just disheartening because this population of people has already gone through so much,” she said. “I just feel like it’s further putting them into a situation where they could be the subject of bullying.”

According to the latest edition of GLSEN’s National School Climate Survey, transgender students are more likely to avoid bathrooms and locker rooms at school because of feeling unsafe or uncomfortable. The survey also found that LGBT students who experienced discrimination, bullying and harassment at school were more than three times as likely to have missed a day in the past month as those who did not. Additionally, LGBT students who experienced discrimination, bullying and harassment at school had lower GPAs than their peers, lower self-esteem and higher levels of depression.

Several transgender students and their parents expressed concern that Sunday’s decision might exacerbate the problems that many of these kids already face.

“I think that this is really detrimental to students,” said 16-year-old Grace Dolan the afternoon before her first day of 11th grade in Washington, D.C. “If we’re not allowed to be who we are, if our schools are not embracing us, we’re not going to be able to excel at the same level as other students.”

Fifteen-year-old Drew Adams knows full well the difficulties of navigating high school when you can’t go to the bathroom. As a transgender student in a conservative district of Florida, Adams can only use one of three gender-neutral bathrooms — all of which, he says, are inconveniently located. Two weeks into his sophomore year, he hasn’t gone to the bathroom at school once.

“I don’t drink until at least lunch, and I don’t eat until I get home,” Adams said.

Despite the ongoing challenges that transgender students will have to face heading into the new school year, many are optimistic they won’t last forever.

“I think that everything happens in baby steps,” said 17-year-old Hunter Keith, a transgender senior in Michigan. “People who are gay and lesbian just finally got the right to marry when it’s been in the media for years. It slowly became more and more normal until there are only a select few that don’t support it.”

“I think that’s going to be the case for people who are transgender,” he said.

History was also on Melissa Baize’s mind as she waited to pick her son up from his first day of school in Fort Worth.

“It takes a lot of time for civil rights or any rights to come full swing,” she said. “It takes people in the community, it takes us as parents of transgender children to have our voices heard.”

Her son, Trevor, had a pretty good first day after all. He sat with a couple of people at lunch, and made a new friend, named Joseph. He also got to the use the boys’ bathroom.

“I’m really excited and really happy they’re letting me use the boys’ bathroom,” Trevor said. “It makes me feel really, really, really happy.”

Correction: An earlier version of this article used an incorrect name for Drew Adams. His last name is Adams, not Kasper.