Schaffner was born in Tokyo, Japan, the son of American missionaries Sarah Horting (née Swords) and Paul Franklin Schaffner, and was raised in Japan. He returned to the United States and graduated from Franklin & Marshall College in Lancaster, Pennsylvania, where he was active in drama. He studied law at Columbia University in New York City but his education was interrupted by service with the United States Navy in World War II during which he served with American amphibious forces in Europe and North Africa. In the latter stages of the war he was sent to the Pacific Far East to serve with the United States Office for Strategic Services.
Returning home after the war, he found work in the television industry with March of Time and then joined the CBS network. He won directing Emmys for his work on the original 1954 CBS teleplay, Twelve Angry Men. Schaffner earned two more Emmy awards for his work on the 1955 TV adaptation of the Broadway play, The Caine Mutiny Court Martial, shown on the anthology series Ford Star Jubilee. He won his fourth Emmy Award for his work on the series, The Defenders.
In the realm of network television, Schaffner also received widespread critical acclaim in 1962 for his groundbreaking collaboration with the First Lady of the United States Jacqueline Kennedy and CBS television's Musical Director Alfredo Antonini in the production of A Tour of the White House with Mrs. John F. Kennedy- a television special which was broadcast to over 80 million viewers worldwide. Schaffner's contributions in this production earned him a nomination in 1963 by the Director's Guild of America USA, for its award in the category of Outstanding Directorial Achievement in Television.
In 1960, he directed Allen Drury's stage play Advise and Consent. His first motion picture The Stripper was praised, and he later made The Best Man, The War Lord, and The Double Man. They were followed by the critical and commercial hit Planet of the Apes. His next film, Patton was a major success for which he won the Academy Award for Best Director and the Directors Guild of America Award for Best Director. Later works included Nicholas and Alexandra, Papillon, Islands in the Stream and The Boys from Brazil.
Schaffner was President of the Directors Guild of America from 1987 until his death in 1989.
Jerry Goldsmith composed the music for seven of his films: The Stripper, Planet of the Apes, Patton, Papillon, Islands in the Stream, The Boys from Brazil and Lionheart. Four of them were nominated for the Academy Award for Best Original Score.
Schaffner twice worked with actors Charlton Heston and Maurice Evans (The War Lord; Planet of the Apes), George C. Scott (Patton; Islands in the Stream) and Laurence Olivier (Nicholas and Alexandra; The Boys from Brazil).
Schaffner married Helen Jane Gilchrist in 1948. The couple had two children, Jennie and Kate.
Schaffner died on July 2, 1989, at the age of 69. He was released 10 days before his death from a hospital where he was being treated for lung cancer.
Screenwriter William Goldman identified Schaffner in 1981 as being one of the three best directors (then living) at handling "scope" (a gift for screen epics) in films. The other two were David Lean and Richard Attenborough.
In 1991 Schaffner's widow Jean established the Franklin J. Schaffner Alumni Medal (colloquially known as the Franklin J. Schaffner Award), which is awarded by the American Film Institute at its annual ceremony to an alumnus of either the AFI Conservatory or the AFI Conservatory Directing Workshop for Women who best embodies the qualities of the late director: talent, taste, dedication and commitment to quality filmmaking.
The moving image collection of Franklin J. Schaffner is held at the Academy Film Archive.