In 1962 the 80th began to transition to the F-105 Thunderchief, and in May 1964 moved from Itazuke to Yokota Air Base, Japan, where it was attached to the 41st Air Division. A few months afterwards, the 8th Tactical Fighter Wing moved to the United States, so the "Headhunters" were reassigned to the 41st Air Division. Stationed at Yokota until 1971, the 80th Tactical Fighter Squadron served under several different parent units over the next few years, including the 6441st Tactical Fighter Wing, 41st Air Division, and 347th Tactical Fighter Wing. The squadron performed two combat deployments to Southeast Asia in 1964 and 1965, serving first for two months at Korat Air Base, Thailand and later for two months at Takhli Air Base, Thailand. For these two combat tours the 80th earned the Vietnam Advisory campaign streamer.

These two deployments made up the total of the 80th Tactical Fighter Squadron's involvement in Vietnam. 80th pilots flew against such major targets as the Hai Nguyen steelPlant, storage facilities at Haipong, northeast and northwest rail lines, Phuc Yen, Kep, and the Doumer Bridge. On 23 August 1967, while flying an F-105 Thunderchief (the largest single-engine fighter ever produced) 1Lt Dave Waldrop (temporarily assigned to the 34th TFS at Korat) gunned down a Mig-17 over North Vietnam. While in Vietnam, the 80th accumulated 7,384 combat missions in Southeast Asia, with 2,657 combat missions over North Vietnam. These missions represent 17,104.4 combat hours over Southeast Asia. Members of the 80th were decorated with 7 Silver Stars, 64 Distinguished Flying Crosses, and 426 Air Medals while deployed to Vietnam.

Sadly, several "Headhunters" remained in Vietnam after the squadron departed. Of these, Quincy Collins, Murphy Neal Jones and Don Heiliger returned home in 1973, but William V. Frederick and Lynn K. Powell are listed as Killed in Action (KIA).

For its involvement, the squadron earned one Battle Honor, the Republic of Vietnam Gallentry Cross (with Palm), and four Air Force Outstanding Unit Citations. During the war, the 80th produced one Ace, Captain Jeff Feinstein, an F-4 WSO with 5 confirmed kills.