Secret History by Donna Tartt I'm not sure it is a "mystery" but anytime someone mentions they like books in academia, I think of this one. This is a great book.

The Blackbird Papers by Dr. Ian Smith. Set in Dartmouth, it's a book that readers either love or hate. I'm in the first group!

Gentlemen and Players by Joanne Harris - I almost didn't even realize it was a mystery until the mystery was solved.

The Lake of Dead Languages AND Arcadia Falls by Carol Goodman.

The Secret History of the Pink Carnation by Lauren Willig combines a grad student doing her doctoral research on Napoleon-era espionage with historical fiction about that era. It has several books in a series following it, as well.

'The Paper Thunderbolt' by Michael Innes (a/k/a the UK literary critic J.I.M. Stewart.) Under his own name, Stewart wrote several Oxford novels: the 'A Staircase in Surrey' quintet, and 'Mungo's Dream.'

Try also: "Oxford Blood" by Antonia Fraser, Carolyn Heilbrun's Amanda Cross series, "Gaudy Night" by Dorothy L. Sayers, "The Professor's House" by Willa Cather, or "The Masters" by C.P. Snow.

"The Physick Book of Deliverance Dane" by Katherine Howe. The protagonist is a doctoral student researching the Salem Witch trials.

The Historian is AWESOME, and Endymion Spring (while a young adult book) wonderful. Both take place, in part, at Oxford.

"Two Murders in my Double Life" by Josef Škvorecký