The organization he leads, the Commander Nazir Group, is alleged to have run training camps, dispatched suicide bombers and provided refuge for al-Qaida fighters, the department said in a statement.
Khan has fought with the Taliban since the late 1990s and was named leader of CNG in January, the United States said. Previously, he was a CNG sub-commander based in Waziristan.
The State Department's designation of Khan blocks him from using any of his property that might be under U.S. jurisdiction and bans U.S. citizens from engaging in any transactions with him.
CNG and one of its sub-commanders, Malang Wazir, were given the global terrorist designation in February.
The group has committed attacks in Pakistan as well as Afghanistan. It took responsibility for a 2008 car bomb attack that killed five Pakistani soldiers and injured 11. It also attacked a Pakistani army camp in May 2011 with missiles and rockets after breaking a ceasefire agreement.