Chalk graffiti saying "Punch Nazis" was written on the bandstand scheduled to be used by the Boston Free Speech Coalition for a "free speech" rally on Saturday.
The city has granted a permit with conditions that will also apply to counter protesters.
The event will be held on Boston Common and will be limited to noon to 2 p.m. instead of the five-hour window organizers had requested.
The rally comes one week after the violence in Charlottesville, Virginia, at a protest put together by white nationalists.
Rally organizers said free speech is the point of the rally here in Boston, and they do not condone violence or hatred.
It's not clear who wrote the graffiti.