Perry once asserted falsely that children with autism often believe they are transgender, saying "they substitute pseudo-science for science. And they leave our children questioning who they truly are." Perry also opposed Title IX protections for transgender students, saying "it should be as simple as Title IX biological girls, period." Perry also attacked shows like "The Babysitters Club" for including transgender characters that teach children about LGBTQ inclusion.

"One again Betsy DeVos is demonstrating her hostility to LGBTQ people. Adding insult to injury, now her department has named an anti-LGBTQ extremist Sarah Perry as the head of its Diversity and Inclusion Council," said Human Rights Campaign President Alphonso David. "LGBTQ youth have known since day one that Betsy DeVos won’t protect them from bullying and discrimination. The idea that someone who calls gender identity 'pseudoscience' and attacks TV shows that promote the inclusion of transgender people is completely disqualifying and violates the fundamental idea of the diversity and inclusion she is tasked with overseeing. This is just one more reason why Donald Trump must be replaced by a pro-equality President and leadership that will look out for LGBTQ students rather than foster an environment that encourages discrimination and exclusion."

Under the direction of DeVos and then Attorney General Jeff Sessions, within days of taking office, the U.S. Departments of Education and Justice revoked the Obama Administration’s guidance detailing schools’ obligations to transgender students under Title IX of the Education Amendments of 1972.

In Sept. 2017, DeVos withdrew vital Title IX guidance related to schools' obligations to address sexual harassment, including sexual violence. LGBTQ people disproportionately experience sexual violence.