Kemeny earned his doctoral degree from Princeton in 1949. As a graduate student, he was Albert Einstein's assistant in mathematics. Einstein was working on unified field theory at the time. Kemeny later wrote:

"People would ask - did you know enough physics to help Einstein? My standard line was: Einstein did not need help in physics. But contrary to popular belief, Einstein did need help in mathematics. By which I do not mean that he wasn't good at mathematics. He was very good at it, but he was not an up-to-date, research-level mathematician. So he needed an assistant for that, and, frankly, I was more up-to-date in mathematics than he was."

At Princeton, Kemeny was drawn to the United World Federalists Movement, which sought a sane, global approach to the new nuclear technology (it was through this movement that he met his future wife, then-Smith student Jean Alexander). Writes J. Laurie Snell, "John was tempted to devote a major part of his time to this program. Einstein told him that he should first make his mark on the world, for then people would listen to him. We have all been rewarded by Kemeny's decision to heed Einstein's advice."