The National Park Service said it did so under federal guidance, which stated non-agency flags could not be officially displayed. The flag came down Sunday night or Monday morning, which sparked outrage among New York politicians and residents.
"Taking down the pride flag was just, it was mean-spirited. It's mean-spirited to a community that often feels under attack," said New York Gov. Kathy Hochul.
Members from the New York City Council's LGBTQIA+ Caucus will hold a rally at 9:30 a.m. Thursday at the monument in Greenwich Village. Then, at 4 p.m., officials said the flag will be re-raised.
The rally is expected to emphasize not only history but what advocates call the need to protect LGBTQ+ visibility at a time of national debate. Speakers will include council members, Assemblyman Tony Simone and other leaders from organizations across the city.
The move could mark the next step in what's becoming a larger debate over federal policy and how historic landmarks are represented moving forward.
The monument is the United States' first dedicated to LGBTQ+ rights and history. It commemorates the birthplace of the modern LGBTQ+ rights movement, sparked by police raids at the Stonewall Inn in 1969. The raids set off three days of protests and riots.
Many local and state politicians have weighed in on the flag's removal.
Gov. Hochul and Manhattan Borough President Brad Hoylman-Sigal were at the monument Wednesday, responding to the flag being taken down.
"If you can't fly the pride flag at the national monument for Stonewall, where can you fly it? So, we are here because that flag has been removed, but it means so much to so many people not just in New York but across the world," said Hoylman-Sigal.
New York City Mayor Zohran Mamdani said he was outraged.
"New York is the birthplace of the modern LGBTQ+ rights movement, and no act of erasure will ever change, or silence, that history," Mamdani posted on social media.
City Council Speaker Julie Menin said she asked the director of the National Park Service for the flag to be restored.
"Stonewall is sacred ground. It is the birthplace of the modern LGBTQ+ rights movement, and the removal of the Pride flag from the Stonewall National Monument is a deliberate and cowardly attempt to erase that history. This is an attack on LGBTQ+ New Yorkers, and we will not stand for it. Our history will not be rewritten, and our rights will not be rolled back," she said in a statement.
References to transgender and queer people were removed from the Stonewall National Monument due to an executive order signed by President Trump. The directive called for the federal government to define sex as only male or female.
Transgender flags were removed from the monument. In addition, the T and Q were struck from the LGBTQ acronym in various places on the website, replaced with "LGB rights movement" and "LGB civil rights."