The Ashmolean, which first opened in 1683, has doubled the space devoted to displaying its world-class collection of art and antiquities, resulting in a sharp increase in visitors from before the refit.
The critically lauded redevelopment, including a new building designed by Rick Mather Architects, has put the museum among the favourites to win the UK's largest single arts prize.
The long-list of 11 museums and galleries also includes the National Army Museum in London for its exhibition "Conflicts of Interest", which focuses on the impact of war on British soldiers and civilians, and the Leach Pottery in St Ives, devoted to Cornwall's prestigious ceramic tradition.
Hampton Court Palace has been nominated for its programme of exhibitions celebrating the 500th anniversary of Henry VIII's accession to the throne.
Kirsty Young, chair of the judges, said the quality of applications for the prize was so high that the judges were unable to restrict themselves to the customary top 10.
She said the list was a "snapshot of the UK's incredible cultural offerings".
The Natural History Museum's Darwin Centre has also been long-listed, hailed as an "awe-inspiring new public space and state-of-the-art science facility".
The other institutions on the list are: the Ulster Museum, Belfast; the Towner in Eastbourne; the Royal Institution of Great Britain; the Herbert Art Gallery and Museum in Coventry; the Great North Museum in Hancock, Newcastle; and the Blists Hill Victorian Town, a 54-acre site which recreates a typical town of the East Shropshire Coalfield in 1900.
The judges will travel the UK to visit each museum before announcing a winner at the Royal Institute of British Architects on June 30.
Stephen Deuchar, director of the Art Fund, said the long list showed the "depth of imagination and drive" of Britain's museums.