According to the directive, bathroom access is a civil rights issue and students must have access to facilities that they feel comfortable using.
"There is no room in our schools for discrimination of any kind, including discrimination against transgender students on the basis of their sex," Attorney General Loretta Lynch said in a statement that accompanied the directive sent by the Education and Justice departments.
The battle over transgender bathroom policies has been raging through the election season, with many Republican lawmakers across the nation apparently just now learning that, like everyone else, transgender people urinate.
Schools that do not comply with the directive will likely face lawsuits, as well as lose federal funding.
"The desire to accommodate others' discomfort cannot justify a policy that singles out and disadvantages a particular class of students," the declaration states.
Along with the directive, the Administration sent out a 25-page primer on how schools can protect LGBT students from bullying and harassment.
On Monday, the Administration also filed a civil rights lawsuit against the state of North Carolina over their discriminatory bathroom law, calling it "impermissibly discriminatory.”
"We see you, we stand with you, and we will do everything we can to protect you," Lynch said to the transgender community, in a powerful statement.