Sapolsky was born in Brooklyn, New York, to immigrants from the Soviet Union. His father, Thomas Sapolsky, was an architect who renovated the restaurants Lüchow's and Lundy's. Robert was raised an Orthodox Jew and spent his time reading about and imagining living with silverback gorillas. By age 12, he was writing fan letters to primatologists. He attended John Dewey High School and, by that time, was reading textbooks on the subject and teaching himself Swahili.
Sapolsky describes himself as an atheist. He said in his acceptance speech for the Emperor Has No Clothes Award, "I was raised in an Orthodox household, and I was raised devoutly religious up until around age 13 or so. In my adolescent years, one of the defining actions in my life was breaking away from all religious belief whatsoever."
In 1978, Sapolsky received his B.A. in biological anthropology, summa cum laude, from Harvard University. He then went to Kenya to study the social behaviors of baboons in the wild. When the Uganda–Tanzania War broke out in the neighboring countries, Sapolsky decided to travel into Uganda to witness the war up close, later commenting, "I was twenty-one and wanted adventure. [...] I was behaving like a late-adolescent male primate." He went to Uganda's capital Kampala, and from there to the border with Zaire (now the Democratic Republic of the Congo), and then back to Kampala, witnessing some fighting, including the Ugandan capital's conquest by the Tanzanian army and its Ugandan rebel allies on 10–11 April 1979. Sapolsky then returned to New York and studied at Rockefeller University, where he received his Ph.D. in neuroendocrinology working in the lab of endocrinologist Bruce McEwen.

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