Barth was born in Leipzig, Germany to Thomas Barth, a professor of geology, and his wife Randi Thomassen. They also had a daughter. Barth and his sister grew up in Norway in an academic family. Their uncle was Edvard Kaurin Barth, a professor of zoology. Fredrik Barth developed an interest in evolution and human origins. When his father was invited to give a lecture at the University of Chicago, the younger man accompanied him and decided to attend the university, enrolling in 1946. He earned an MA in paleoanthropology and archaeology in 1949.