The teen allegedly threw a rock at the New England Holocaust Memorial, shattering a glass panel at around 6:40 pm (2240 GMT) on Monday, before being detained by two bystanders, police said.
Shattered glass littered the ground next to the damaged panel.
The suspect would be charged with willful and malicious destruction of property, police said. Officers from the civil rights unit were investigating to determine if additional charges are pending.
"Boston stands up against hate. I'm saddened to see such a despicable action in this great city," said Mayor Marty Walsh.
The incident came two days after a woman was killed when a suspected Nazi sympathizer plowed a car into a crowd of anti-racism protesters after a violent rally by neo-Nazis and white supremacists in Charlottesville, Virginia.
It was the second time in less than two months that the Boston Holocaust memorial has been vandalized, officials confirmed. Another suspect was charged last time.
The memorial has six glass towers, representing the six million Jews murdered in the Holocaust, the six main death camps and the six years, 1939-1945, during which the infamous "Final Solution" took place.
Boston is the largest city in the northeastern state of Massachusetts.
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