The rally on Boston Common, which attracted only a small crowd, disbanded early and the participants were escorted out by police.
The conservative rally organizers had said they would not give a platform to racism or bigotry.
Tensions are high after violent demonstrations in Charlottesville, Virgina, last weekend turned deadly.
Up to 30,000 people attended the counter-protest, The Boston Herald reported. Demonstrators had gathered at a Boston sports centre and then marched en masse to the common.
Many wore stickers with the face of Heather Heyer, who died when a car was driven into a crowd of counter-protesters at last Saturday’s far-right rally in Charlottesville.
The crowd chanted “No Nazis, no KKK, no fascists in the USA!” and carried banners with slogans such as “Stop pretending your racism is patriotism”.
Hundreds of police, many on cycles, were deployed but no violence was reported. Large vehicles were positioned along with concrete barriers to prevent access to the park.
The organizers of the rally said that “misinformation in the media” was “likening our organization to those that ran the Charlottesville rally”.
“While we maintain that every individual is entitled to their freedom of speech and defend that basic human right, we will not be offering our platform to racism or bigotry,” the group wrote on a Facebook page dedicated to the event.
“We denounce the politics of supremacy and violence.”
The list of speakers for the free speech event changed a number of times in previous days. At times it included speakers who have been associated with the far right.
The violence in Charlottesville began with a protest and counter-protest over the planned removal of a statue of Confederate commander General Robert E. Lee.
In the aftermath, Confederate statues across America have come under renewed scrutiny.
On August 19, Duke University in North Carolina removed a statue of Robert E. Lee from its chapel entrance, following vandalism earlier in the week.
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