Benzer was born in the South Bronx to Meir Benzer and Eva Naidorf, both Jews from Poland. He had two older sisters, and his parents favored him as the only boy. One of Benzer's earliest scientific experiences was dissecting frogs he had caught as a boy. In an interview at Caltech, Benzer also remembered receiving a microscope for his 13th birthday, “and that opened up the whole world.” The book Arrowsmith by Sinclair Lewis heavily influenced the young Benzer, and he even imitated the handwriting of Max Gottlieb, a scientist character in the novel. Benzer graduated from New Utrecht High School at 15 years old.