He was the son of Lili Conrat and Professor Ludwig Fraenkel, director of the Women's Clinic of the University of Breslau.

His father was a prominent gynecologist and medical researcher who published regarding endocrine function, social gynecology, and sexology during the first decades of the 20th century, and was one of many scientists summarily dismissed from their positions by the Nazis.

In the 1940s Fraenkel-Conrat visited his sister and brother-in-law, biochemist Karl Slotta, a pioneer in the study of progesterone, estriol, and medical use of venom, who was then director of the Chemical Institute of the Instituto Butantan in São Paulo, Brazil, from 1935 to 1948.

He worked at a number of institutes before joining the faculty at the University of California, Berkeley in 1952 where he remained until his death.

In 1955 he and biophysicist Robley Williams showed that a functional virus could be created out of purified RNA and a protein coat.