[4] Penny's academic career began with a research fellowship at Clare Hall, Cambridge, after which he went on to teach art history at Manchester University.
While still in his early thirties, Penny was appointed to the Slade Professorship at Oxford University and to a senior research fellowship at King's College, Cambridge.
Shortly afterwards, in 1991, he identified the Madonna of the Pinks belonging to the Duke of Northumberland as a genuine Raphael, and not a copy of a lost original as was previously supposed.
Following Saumarez Smith's early resignation from his post, Penny was once again a candidate for heading the London National Gallery, and this time he succeeded.
He has also published books, exhibition catalogues, and articles on picture frames and Italian Renaissance painting, and on Raphael, Sir Joshua Reynolds, and Richard Payne Knight.