Duffy's departure from News International, publisher of The Scottish Sun and News of the World, comes as the newspaper publisher is undergoing an executive restructure north of the border.
Duffy was previously business director at CBS Outdoor Scotland but left the role in December last year.
He spent less than two years in his role at CBS Outdoor.
He took up his role at News International in February this year. It is unclear if Duffy is to be replaced in the role.
Separately, Steven Walker, the general manager for News International Scotland, which is responsible for The Times, The Sunday Times, The Sun and the News of the World north of the border, is stepping down.
Sales director Elaine Ward-Fincham is also leaving the publisher north of the border. News International says the two departures are part of a review of its sales operations.
Sandra Tinker, the head of News International's advertising team in Manchester, is to replace Tinker.
It is understood that News International is looking to shift its commercial activity from Glasgow to Manchester as it looks to save costs.
News International confirmed all the departures but declined to comment further.
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