The Obama-era rule directed public schools to allow transgender pupils to use toilets of their gender identity. But critics said that guidance was government overreach which threatened other students' privacy and safety.
White House spokesman Sean Spicer said Mr Trump firmly believes "this is a states' rights issue".
"I would expect further guidance to come out on that today," he told a news conference.
Though the Obama-era order will be rescinded, anti-bullying safeguards are expected to remain in place, the AP news agency reported, citing a government official.