Agar was born in Chicago, Illinois, the son of Lillian (née Rogers) and John George Agar Sr., a meat packer. He was educated at the Harvard School for Boys in Chicago and Lake Forest Academy in Lake Forest, Illinois. He graduated from Trinity-Pawling Preparatory School in Pawling, New York, but did not attend college. He and his family moved from Chicago to Los Angeles in 1942, after his father's death.

During World War II, Agar joined the Navy Air Corps, had basic training in Texas, and instructed in physical training at March Field in Riverside, California. He later transferred to the United States Army Air Corps. He was a sergeant at the time he left the AAF in 1946.

Agar made his film debut as Temple's love interest in Fort Apache (1948), a John Ford western for RKO starring John Wayne and Henry Fonda. It was a financial and critical success.

Even more popular was the World War II film Sands of Iwo Jima (1949) where Agar supported John Wayne. Made by Republic Pictures, it was a sizeable hit, earning Wayne an Oscar nomination and getting Agar some good reviews.

In 1950 Agar was fined for reckless driving. In 1951 Agar was jailed for five months for drunk driving. He was released after 60 days on probation. In 1953 Agar was arrested for drunk driving again and was sentenced to 120 days in prison. In 1960 he was again arrested for drunk driving.

Agar remarried in 1951 to model Loretta Barnett Combs (1922–2000). They tried to elope but officials refused to marry them for an hour because Agar had been drinking. They remained married for 49 years until her death in 2000. They had two sons, Martin Agar and John G. Agar, III.

Agar was third billed in Woman of the North Country (1952), a Western for Republic, and so starred in Man of Conflict (1953), an independent drama with Edward Arnold.

In 1954 Agar signed a seven-year contract with Universal. He began the association with Revenge of the Creature (1955), the popular first sequel to Creature from the Black Lagoon (1954); it was produced by william Alland and directed by Jack Arnold.

Agar made another science fiction film, Tarantula (1955), made by Alland and Arnold, which was popular and became a cult favorite.

Universal starred him in a Western, Star in the Dust (1956), produced by Albert Zugsmith. A new company, American International Pictures, borrowed Agar for a Western, Flesh and the Spur (1956). Then he went back to Universal for The Mole People (1956), produced by Alland.

Agar remained in demand for low budget science fiction, horror and Western films. He starred in The Daughter of Dr. Jekyll (1957) for Edgar G. Ulmer at Allied Artists, then made The Brain from Planet Arous (1957) for Howco International.

Agar did Invisible Invaders (1958) for Director Edward L. Cahn who had made Jet Attack.

Agar could be seen in Journey to the Seventh Planet (1962), The Young and The Brave (1963), Of Love and Desire (1963), Law of the Lawless (1963), Stage to Thunder Rock (1965), Young Fury (1965), Johnny Reno (1966), Women of the Prehistoric Planet (1967), and Waco (1966).

Agar made some films for Larry Buchanan at AIP, Curse of the Swamp Creature (1966), Zontar, the Thing from Venus (1966) and Hell Raiders (1968). He had the lead in Night Fright (1967).

Agar had small parts in some studio films like The St. Valentine's Day Massacre (1967), and three with John Wayne: The Undefeated (1969), Chisum (1970), and Big Jake (1971).

Agar's last prominent roles were small roles in King Kong (1976) and Miracle Mile (1988).

The Seattle band The Young Fresh Fellows recorded the song "The New John Agar" on the Topsy Turvy album in 1985.

Agar died on April 7, 2002, at Burbank, California of complications from emphysema. He was 81. He was buried beside his wife at Riverside National Cemetery in Riverside, California. He was survived by his three children, four grandchildren, and two brothers.