"No Ku Klux Klan, no fascists, no racists" the students from Manhattan and Queens shouted in turn, alternating their cries with: "Say it loud, say it clear, refugees are welcome here."
In Washington, several hundred high school students marched on the Mall, the grassy esplanade that runs from the Capitol to the Lincoln Memorial, heading toward the White House.
The protests came one day after hundreds of students walked out of classrooms to rally against Donald Trump's election in Portland, Oregon; Silver Spring, Maryland; and Los Angeles.
Trump Tower has been the focus of protests every day since the New York billionaire's election a week ago.
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Grace said they were a reminder to local officials that "just because Trump is elected does not mean the policies he talked about during the election have to go through."
Some in the crowd shouted "My body my choice," giving voice to concerns about reverses on women's rights to abortion under Trump, who has vowed to put pro-life justices on the high court.
A woman's right to end a pregnancy was established under the Supreme Court's landmark 1973 Roe v Wade decision. If a more conservative court overturns it, it would fall to individual states to decide whether to allow abortions.
"Being in NYC it won't really affect us but it will affect a lot of people in other states that don't have the same privilege," Greta, age 17, told AFP.
Another protester told AFP she hoped the US system of using an electoral college to elect presidents could be changed. Trump won the White House by picking up the most electoral -- even though rival Hillary Clinton's lead in the popular vote.
Protests have been held daily across the United States since Trump won last Tuesday's election.
Dozens of police stood guard around Trump Tower, where Trump has spent most of his time since the election meeting with advisors on his new administration.