Linklater's career in journalism began in 1964 as a reporter with the Daily Express. This was followed by a period as reporter, then editor of the Londoner's Diary on the Evening Standard, before he moved to The Sunday Times in 1969, where he was magazine editor, news editor and executive editor. He had a central role in the Hitler diaries scandal. He remained at The Sunday Times until 1983. This was followed by three years at The Observer, where he was Managing Editor before he was recruited to launch and edit the London Daily News, a short-lived newspaper owned by Robert Maxwell. Linklater returned to Scotland at the start of 1988 to become editor of The Scotsman, running the newspaper until 1994, when he left to become a freelance writer, and columnist for The Times. In 2007 he was appointed Scottish Editor of The Times, a position he held until 2012. Since then he has continued as a regular contributor to The Times. From 1998 to 2007, he wrote a weekly column for The Scotsman's sister paper, Scotland on Sunday. Between 1994 and 1997 he presented the weekly discussion programme Eye to Eye on BBC Radio Scotland, and has written a number of books, including an account of the hoax autobiography of Howard Hughes, a life of Jeremy Thorpe, and an investigation of the Nazi war criminalKlaus Barbie. He has also written books on Scottish history and politics. He was appointed as chairman of the Scottish Arts Council in 1996, holding the post for five years, and is currently chairman of the Little Sparta Trust, which maintains Little Sparta, the garden of the late Ian Hamilton Finlay, in the Pentland Hills. He is President of the Saltire Society, and Chairman of Horsecross Arts Limited, which manages Perth Concert Hall and Perth Theatre. Linklater was a candidate for the position of Rector of the University of Aberdeen in 1999 and Rector of University of Edinburgh in the 2006 election, finishing second, behind Scottish Green Party politician Mark Ballard. He is a Trustee of his wife's family estate in Perthshire. In the 2001 Teissier affair, in which Elizabeth Teissier was awarded a doctorate in sociology for a thesis defending astrology, Linklater succinctly summarised that "the core problem of the incident was that ' really believes in astrology. And there is the rub. If you seriously believe that the stars rule our lives, you have abandoned the most basic tenet of science which is knowledge obtained by observation and experiment.'" Linklater was criticised for making Teissier into an "ontological criminal: what mattered for Teissier's academic qualification was not the quality of her work but her private beliefs" based on Linklater's alleged position that "the only source of knowledge can be science; the social sciences and humanities are automatically inferior explanatory models." The criticisms of Teissier's work, however, were not based on her astrological beliefs but on the poor quality of its scientific content and lack of legitimate sociology. Linklater lives in the New Town of Edinburgh, with his wife Veronica, a Liberal Democratlife peer. Their house was badly damaged by a fire on New Year's Day 2006, destroying much of his art collection, including paintings by Samuel Peploe and William George Gillies. Linklater was appointed Commander of the Order of the British Empire in the 2013 New Year Honours for services to the arts and media in Scotland.
