Michael Reinoehl, 48, brandished a gun and was killed as a federal taskforce attempted to apprehend him in Lacey, Washington state, an official said.
He was the prime suspect in the killing of Aaron Jay Danielson, who was shot in the chest on Saturday night in the troubled US city.
Authorities said the 39-year-old was shot during clashes between supporters of US President Donald Trump and counter-protesters.
It was not clear if the shooting was linked to fights that broke out as a caravan of about 600 vehicles was confronted by protesters in the city centre.
Federal agents from the FBI and the US Marshals Service had located Reinoehl on Thursday after a warrant was issued for his arrest.
During the encounter, he was shot by a law enforcement officer working on the taskforce after pulling a gun, the official said.
Reinoehl had described himself in a social media post as “100% ANTIFA”, suggested the tactics of counter-protesters amounted to “warfare”, and had been shot at one protest and cited for having a gun at another.
He had been been a regular presence at anti-racism demonstrations in Portland.
