Jeremy Knowles attended Magdalen College School, Oxford, and then served as a Pilot Officer in the Royal Air Force from 1953-55. He read Chemistry at Balliol College, Oxford, subsequently being elected a Harmsworth Scholar at Merton and then a Research Lecturer at Christ Church. Following a postdoctoral fellowship at Caltech, he returned to Oxford in 1962 as Fellow and Tutor of Wadham College, and was appointed to a University Lectureship in 1966. He was a Visiting Professor at Yale in the Departments of Molecular Biophysics and of Chemistry in 1969 and 1971, and Sloan Visiting Professor at Harvard in 1973. In 1974, he joined the Harvard Faculty as Professor of Chemistry, and became the Amory Houghton Professor of Chemistry and Biochemistry in 1979. In 1983-84 he was Newton-Abraham Visiting Professor at Oxford. He was appointed Dean of the Faculty of Arts and Sciences in 1991. He stepped down from the deanship and returned to the Faculty in 2002. In 2003, he was named Harvard University Distinguished Service Professor. Professor Knowels is on leave for the fall semester of the 2007-08 academic year.

Knowles was elected a Fellow of the Royal Society in 1977, and of the American Academy of Arts and Sciences in 1982. He holds Honorary Fellowships at Balliol College and Wadham College, Oxford. In 1988 he was elected a Foreign Associate of the National Academy of Sciences, and a member of the American Philosophical Society. He has been awarded the Charmian Medal of the Royal Society of Chemistry, the Bader Award and an Arthur Cope Scholar Award from the American Chemical Society, the Davy Medal from the Royal Society, the Prelog Medal, the Robert A. Welch Award, and the Repligen Award and the Nakanishi Prize. He was appointed Commander of the British Empire in the Queen's Birthday Honours of 1993, and received the Harvard Medal in 2002. He is a Trustee of the Howard Hughes Medical Institute.