The department said Abubakar Shekau, Abubakar Adam Kambar and Khalid al-Barnawi received the designation under an existing presidential executive order, CNN reported.
They were referred to as "specially designated global terrorists."
"These designations demonstrate the United States' resolve in diminishing the capacity of Boko Haram to execute violent attacks," the department said in a written statement Thursday.
Boko Haram has been waging a campaign of bombings of Christian churches that have killed hundreds of people in Nigeria.
The Boko Haram members were referred to as "global terrorists."
The group is blamed for an attack on a United National building in the Nigerian capital of Abuja last year that killed at least 23 people.
Boko Haram often refers to itself as the Nigerian Taliban and seeks to overthrow the Nigerian government and replace it with a regime based on Islamic law.