The decision is based on the presidential decree on "a pattern of political violence designed to suppress lawful political activity and prevent the principles of the rule of law".
The message comes after the murder of right-wing debater Charlie Kirk earlier in September.
Antifa - short for "anti-fascists" - is used as an umbrella term for a number of groups and is not a single organization, but rather a political ideology according to experts.
Trump's former FBI chief, Christopher Wray, described Antifa in 2020 as an ideology and not an organization. He believed that the movement lacks the hierarchical structure that would normally make it possible for the federal government to designate it as a terrorist group.