Agar was born in Chicago, Illinois, the son of Lillian (née Rogers) and John 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 he served in the Army Air Forces, mostly at the March Field in Riverside, California, serving as a physical fitness instructor. He was a sergeant at the time he left the AAF in 1946. Agar’s sister was a schoolmate of Shirley Temple. In 1944 Agar escorted Temple to a party held by her boss at the time, David O. Selznick. The two fell in love and were married in 1945. Selznick signed Agar to a five-year acting contract starting at $150 a week, including acting lessons. Agar and Temple worked together in Fort Apache and Adventure in Baltimore. The first of these, where they supported John Wayne, was particularly successful. Agar later reunited with Wayne in two more hits, She Wore a Yellow Ribbon and The Sands of Iwo Jima. Agar and Temple had a daughter together, Linda Susan Agar, b. 1948, (who was later known as Susan Black, taking the surname of her stepfather Charles Alden Black). However, the marriage foundered, in part because of Agar’s drinking (he had been arrested for drunk driving) and in part because of pressures of their high public profile. Temple sued for divorce on the grounds of mental cruelty in 1949.

Agar’s career suffered in the wake of his divorce, but he developed a niche playing leading men in low-budget science fiction, Western, and horror movies in the 1950s and 1960s. John Wayne gave him several supporting roles in the late 1960s and early 1970s. In later years he worked extensively in television. “I don’t resent being identified with B science fiction movies at all,” Agar later said. “Why should I? Even though they were not considered top of the line, for those people that like sci-fi, I guess they were fun. My whole feeling about working as an actor is, if I give anybody any enjoyment, I’m doing my job, and that’s what counts.” After his divorce from Temple, Agar remarried in 1951 to model Loretta Barnett Combs (1922–2000). They remained married until her death in 2000. They had two sons, Martin Agar and John G. Agar, III. Agar died on April 7, 2002 at Burbank, California of complications from emphysema. He was buried beside his wife at Riverside National Cemetery in Riverside, California. He was survived by his three children.