Miller, 57, who currently serves as commander of Joint Special Operations Command, also received his fourth star as part of the confirmation.
Miller is expected to take over both NATO’s train, advice and assist mission and the U.S.’s separate counterterrorism mission in Afghanistan in the fall.
He replaces Army Gen. John Nicholson, who after more than two years in charge became the U.S.’s longest-serving commander of the 17-year war.
During his confirmation hearing, Miller endorsed the U.S.’s revamped war strategy which has allowed for more airstrikes against Taliban targets but said he didn’t foresee an end to the conflict anytime soon.
“I can’t guarantee you any timeline or an end date,” he told the Senate Armed Services Committee earlier in June, adding that withdrawal from Afghanistan could allow extremist groups like the Islamic State to strengthen and carry out attacks on U.S. soil.
Miller’s confirmation was one of several military and diplomatic confirmations Thursday.