The arrests were largely for disorderly conduct including some for assault and battery.
The event, which was billed as a “free speech” rally, ended early after thousands of counter-protesters overwhelmed the crowds.
An estimated 40,000 people packed into the streets around the nation’s oldest park, most of whom were anti-fascist demonstrators who sought to drown out the far-right.
Chris Hood, a free speech rally attendee, said people were unfairly making it seem like the rally was going to be “a white supremacist Klan rally”.
“That was never the intention,” he said.
“We’ve only come here to promote free speech on college campuses, free speech on social media for conservative, right-wing speakers, and we have no intention of violence.”
Groups and activists such as the Black Lives Matter movement organised the counter-rally, with some carrying signs with messages such as “No Trump. No KKK. No racist USA” and “Americans against hate”.
Boston’s police department tweeted that protesters were throwing bottles, urine and rocks at them and asked people publicly to refrain from doing so.
They marched through the city to Boston Common, where many gathered near a bandstand abandoned early by the conservatives who had planned to deliver a series of speeches.
The rally’s speakers could not be heard due to the shouts of those protesting against them, and they eventually wrapped up about an hour earlier than planned.
Organisers of the initial event had publicly distanced themselves from white supremacists and others who spurred violence in Charlottesville, Virginia on 12 August which left one woman dead.
Robert Paulson, another rally attendee, said there was definitely a lot of tension.
“They believe that we’re Nazis and KKK down here. That’s what they think, a lot of them. It’s not true. A lot of the people down here just love the United States, are here to promote free speech,” he said.
President Donald Trump had complimented Boston police, tweeting: “Looks like many anti-police agitators in Boston. Police are looking tough and smart! Thank you.”
The President was criticised in the wake of Charlottesville after insisting there was “blame on both sides”, and failing initially to condemn white supremacists.