Scrutton was born in Batley, West Riding of Yorkshire and was brought up in Cleckheaton where he went to Whitcliffe Mount School. Scrutton graduated from King's College London with a first class Bachelor of Science degree in Biochemistry in 1985. He was a Benefactors' Scholar at St John's College, Cambridge where he completed his doctoral research (PhD) in 1988 supervised by Richard Perham. He was a Research Fellow of St John's College, Cambridge (1989–92) and a Fellow / Director of Studies at Churchill College, Cambridge (1992–95). He was awarded a Doctor of Science (ScD) degree in 2003 by the University of Cambridge.
