Schaffner was born in Tokyo, Japan, the son of American missionaries Sarah Horting (née Swords) and Paul Franklin Schaffner, and was raised in Japan.
The Schaffners returned to the United States and settled in Lancaster, Pennsylvania when Franklin Schaffner was 5 years old. Franklin Schaffner attended J.P. McCaskey High School, where he appeared as Mr. Darcy in the school's production of Pride and Prejudice. In 1938, he graduated as valedictorian of McCaskey High School's first graduating class.
Schaffner graduated from Franklin & Marshall College (F&M) in Lancaster. As a student, Schaffner was active in the drama program at F&M's Green Room Theatre, where he appeared in eleven plays and served as president of the Green Room Club. He then 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 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.

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