John Quincy Stilwell was born in Columbia, South Carolina, on September 20, 1933 to Edna Douglass and James Raymond Stilwell. He attended public schools in the Southeast and briefly in New Jersey, graduating in 1951 from the High School of Charleston, South Carolina.

In 1954 he received an A.B. degree from the University of North Carolina at Chapel Hill with a major in English History and a minor in Naval Science, and was commissioned an Ensign in the United States Navy. Stilwell was on active duty with the Atlantic Fleet as Operations Officer and Acting Executive Officer of U.S.S. Basilone (DDE 824) until his release in May 1958. In September of that year he entered Columbia University Law School in New York City.