Kendrew, who was born at Oxford, graduated in natural science from Cambridge University in 1939. He spent the war years working for the Ministry of Aircraft Production, becoming an honorary wing commander in 1944. In 1946 he joined Max Perutz at Cambridge and, like Perutz, used x-ray diffraction techniques to study the crystalline structure of proteins, particularly that of the muscle protein myoglobin. X-ray diffraction, or crystallography, involves placing a crystal in front of a photographic plate and rotating the crystal in a beam of x-rays. The pattern of dots that is formed on the plate by the x-rays can be analyzed to find the positions of the atoms in the crystal. The technique had been used successfully to show the structures of small molecules but Kendrew's progress with the much larger myoglobin structure was slow, especially since diffraction patterns yield no information on the phases of the directed x-rays. However, in 1953 Perutz made a breakthrough by incorporating atoms of heavy elements into the protein crystals. Kendrew modified this new method and applied it successfully in his myoglobin studies, so that four years later he had built up a rough model of the three-dimensional structure of myoglobin. By 1959 he had greatly clarified the structure and could pinpoint most of the atoms.

Kendrew and Perutz received the 1962 Nobel Prize for chemistry for their work on protein structure. Kendrew was knighted in 1974 and served as director general of the European Molecular Biology Laboratory in Heidelberg from 1975 to 1982.