An experienced Scottish news editor, and previously a courts and crime reporter, Mr Wilkie died at home on Christmas Day with his wife Irina at his side.
She said in a short statement posted on social media: “My husband passed away today ... he was the most wonderful person I’ve ever known.”
Mr Wilkie had worked for the Scotsman group since November 2018.
He joined the company as deputy news editor with the Edinburgh Evening News before later becoming Live Editor for the Edinburgh team.
Mr Wilkie played a key mentoring role with a host of reporters across the Scotland newsroom. He was critical to expanding the court and crime coverage of both The Scotsman and the Edinburgh Evening News.
Scotsman editor Neil McIntosh said: “Stephen meant an awful lot to us.
"A brilliant professional, he was born to be in a newsroom, and was an immensely caring, compassionate figure.
"He offered countless words of advice to colleagues, from junior journalists in their early years to senior staff taking on new roles. From practical advice to a gentle word of encouragement, his support was always welcome and timed to perfection. His razor-sharp intellect brought insight and wit to our news meetings every day.”
Mr McIntosh added: “Stephen and Irina clearly shared a deep bond. Now, all our thoughts are with her, their family and friends, all of whom will be feeling his loss keenly.”
Mr Wilkie had started out as a trainee at the-then Glasgow Herald in 1983, before moving on to the Glasgow Courts Press Agency later the same year.
In 1984, he joined a freelance agency based in the lobby at Glasgow City Chambers.
He then spent two years in weeklies while shifting at the Scottish Sun from its launch in 1986 and moved up from reporter to crime reporter before joining the Record.
Mr Wilkie later returned to the Sun, moved to the News of the World, had a spell back in weeklies in a new elevated role and joined the Daily Express & Daily Star as reporter/news editor.