Suppes was born on March 17, 1922, in Tulsa, Oklahoma. He grew up as an only child, later with a half brother George who was born in 1943 after Patrick had entered the army. His grandfather, C.E. Suppes, had moved to Oklahoma from Ohio. Suppes' father and grandfather were independent oil men. His mother died when he was a young boy. He was raised by his stepmother, who married his father before he was six years old. His parents did not have much formal education.

Suppes initially graduated with a B.S. in Meteorology from the University of Chicago in 1943, and was stationed at the Solomon Islands during WWII.

He was discharged from the Army Air Force in 1946.

In January 1947, he entered Columbia University as a graduate student in philosophy as a student of Ernest Nagel and received a PhD in 1950.

In 1952 he went to Stanford University, and from 1959 to 1992 he was the director of the Institute for Mathematical Studies in the Social Sciences (IMSSS). (He was later to become the Lucie Stern Professor of Philosophy, Emeritus, at Stanford)

In the 1960s, Suppes and Richard C. Atkinson (the future president of the University of California) conducted experiments in using computers to teach math and reading to schoolchildren in the Palo Alto area. Stanford's Education Program for Gifted Youth and Computer Curriculum Corporation (CCC, now named Pearson Education Technologies) is an indirect descendant of those early experiments.

One computer used in Suppes and Atkinson's Computer-assisted Instruction (CAI) experiments was the specialized IBM 1500 Instructional System. Seeded by a research grant in 1964 from the U.S. Department of Education to the Institute for Mathematical Studies in the Social Sciences at Stanford University, the IBM 1500 CAI system was initially prototyped at the Brentwood Elementary School (Ravenswood City School District) in East Palo Alto, California by Suppes. The students first used the system in 1966.