He will share the role with Will Lewis, and will eventually replace Neil Darbyshire, who is standing down but staying within the Daily Telegraph's senior editorial team.
MacGregor, who began his career at South West News Agency in Bristol, presided over the launch of the Metro free newspaper in London, where he was editor in 2001, before moving to the Evening Standard, where he has been deputy editor for the last four and a half years working under editor Veronica Wadley.
His appointment comes as the Daily Telegraph continues without an editor following the departure of Martin Newland in November.
John Bryant, editor-in-chief at the Daily Telegraph, said: "Ian has an extensive hard news background. Brilliant news coverage has always been at the core of the Daily Telegraph's reputation and we are delighted he has agreed to join us."
After finishing at Edinburgh University, MacGregor worked at the Southern Evening Echo in Southampton before joining the Press Association.
He became education correspondent at the Daily Express and moved to the Daily Mail in 1993, where he was news editor for two years.
Last month it was reported that the Daily Telegraph, which is owned by the Barclay brothers, was planning to trial a tabloid edition at the end of the year in East Anglia alongside its current broadsheet format.
It is understood that Lewis, who is overseeing the newspaper's move to new offices in London's Victoria, is keen to trial a tabloid format as part of its wider plans to "digitally reinvent itself".
The Daily Telegraph was down 7% to 2,061,000 in the latest ABC figures.
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