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'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 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 (Agar's film debut) 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 Sands of Iwo Jima.
Agar and Temple had a daughter together, Linda Susan Agar, born 1948 (who was later known as Susan Black, taking the surname of her stepfather, Charles Alden Black). However, the marriage floundered, 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. The two were divorced on December 7, 1950.
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 he was arrested for drunk driving again and was sentenced to 120 days in prison.
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."
In 1954 Agar signed a seven-year contract with Universal.
In 1960 he was again arrested for drunk driving.
The television series Mystery Science Theater 3000 has made fun of several of Agar's films, including The Mole People and Lost Continent.
After his divorce from Temple, Agar remarried in 1951 to model Loretta Barnett Combs (1922–2000). They remained married for 49 years 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 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.Agar made six movies with John Wayne: Fort Apache, Sands of Iwo Jima, She Wore a Yellow Ribbon, The Undefeated, Chisum, and Big Jake.
The Seattle band The Young Fresh Fellows recorded the song "The New John Agar" on the Topsy Turvy album in 1985.
Perry Mason (1959) - episode - The Case of the Caretaker's Cat - Kenneth Baxter
Rawhide (1959) - episode - Incident at the Buffalo Smokehouse - Lon Grant
Destination Space (1959) - unsold pilot
Rawhide (1960) - episode - Incident of the Slavemaster - Mike Anderson
Bat Masterson (1961) - episode - Farmer with a Badge - Sam Phelps
Ripcord (1961) - episode - Chuting Stars - Warren Officer Frank Pierson
Lawman (1962) - episode - The Witness - Jim Martin
Death Valley Days (1963) - episode - Pioneer Doctor - Dr. Edwards
The Virginian (1964) - episode - Another's Footsteps - Tom Anders
Branded (1965) - episode - $10,000 for Durango - The Sheriff
Family Affair (1967) - episode - What Did You Do in the West, Uncle? - Gabe
Hondo (1967) - episode - Hondo and the Judas - Frank James
The Virginian - episode - The Mustangers - Joe Williams
Charlie's Angels (1976) - episode - Target: Angels - Col. Blaylock
Highway to Heaven (1984) - episode - The Return of the Masked Rider - Morton Clay
The Making of 'Sands of Iwo Jima (1993) - Video Documentary Short - Himself