Santer was educated at Marlborough College and Queens’ College, Cambridge before his ordination in 1964.
After being a curate he was a tutor at Ripon College Cuddesdon. Dean and Fellow of Clare College, Cambridge. Assistant lecturer in divinity at the University of Cambridge and finally Principal of Westcott House, Cambridge before his ordination to the episcopate as area Bishop of Kensington in 1981.
After six years at Kensington, he was translated to be the Bishop of Birmingham.
During this time he took part in the second phase of the ecumenical discussions of the Anglican—Roman Catholic International Commission and was embroiled in controversy over the use of the term "Winterval", which he opposed. In retirement he served as an assistant bishop in the Diocese of Worcester.
Married Henriette Cornelia Weststrate in 1964.