Mr Ovenden will succeed Dr Sarah Thomas, and will become a Fellow of Balliol College.
As well as managing the day-to-day running of the Broad Street library, he will take on the stewardship of combined collections numbering more than 11 million printed items, in addition to 50,000 e-journals.
Mr Ovenden has worked at the Bodleian since 2003 and has held the position of Interim Bodley’s Librarian since August.
He said: “This is a profound honour and privilege, as we seek to develop our services, build our collections and support our staff through the rapidly changing environment of scholarship and information provision.
“The Bodleian stands at the heart of the university, working in partnership with all of the academic disciplines and supporting the international community of scholars as well as the citizens of Oxford and worldwide who access the Bodleian digitally or visit our exhibitions.”
Prof Andrew Hamilton, vice-chancellor of the University, said: “We are delighted that Richard Ovenden has been appointed to the historic post of Bodley’s Librarian.
“Richard’s experience, both in major libraries elsewhere and more recently as a leading member of Dr Thomas’s team, makes him ideally placed to take forward the next phase of these developments.”