Fried became a member of the National Academy of Sciences in 1971. He became a member of the American Academy of Arts and Sciences in 1981. He received the Medicinal Chemistry Award in 1974 from the American Chemical Society. He also received the Alfred Burger Award in Medicinal Chemistry in 1996. 
He also received the Gregory Pincus Medal from the Worcester Foundation for Experimental Biology and the Roussel Prize from the Roussel Scientific Institute in Paris in 1994.
Bristol-Myers Squibb and the University of Chicago launched in 1990 the first of a series of annual Josef Fried Symposia of Bioorganic Chemistry. Fried is a member of the Medicinal Chemistry Hall of Fame.