One of three children of Dan Rory MacIntyre and Alice Donohue, he was raised in Port Hastings, Nova Scotia. As a miner, his father was rarely at home. MacIntyre has said, "The old fellow decided the family would stay in the community and he would go away and stay as long as it took. ... My mother was a teacher and my sister and I stayed with her.”

After high school, MacIntyre moved to Antigonish, Nova Scotia where he obtained a Bachelor of Arts degree from St. Francis Xavier University in 1964. He also studied at St. Mary's University and the University of King's College in Halifax. From 1964 to 1967 he worked for the Halifax Herald as a parliamentary reporter in Ottawa. He continued in the same role with the Financial Times of Canada from 1967 to 1970. He was drawn back to Cape Breton after the death of his father in 1970 and for the next six years he lived there and worked as a correspondent for the Chronicle Herald.

He joined the Canadian Broadcasting Corporation in Halifax in 1976 and for three years he hosted a regional public affairs show called The MacIntyre File. It was while with this program that he launched a successful legal challenge before the Supreme Court of Nova Scotia over access to affidavits and documents relating to search warrants. Later heard before the Supreme Court of Canada, the successful suit was a landmark case which set a precedent in support of public and media access to information in Canada.

In 1980, MacIntyre moved to Toronto, where he still resides, to work as a producer and journalist on CBC’s new flagship news program, The Journal. This appointment took him around the world preparing documentary reports on international affairs, preparing such notable features as "Dirty Sky, Dying Water" (about acid rain). Various jobs at the CBC through the eighties culminated in his appointment in 1990 as co-host of the weekly newsmagazine the fifth estate, with which he is still involved. In addition, he is a frequent guest host of The Current on CBC Radio One.

Stories

For the fifth estate, he has written numerous investigative reports often with producer Neil Docherty. Many of the shows have also appeared on Frontline. Examples of his stories include:

• "To Sell a War" (1992). The film is about a public relations campaign to gain public opinion support for the First Gulf War. It won an International Emmy and a Gemini Award.
• "The Trouble With Evan" (1994). This film, about the psychological abuse of a child by his parents, was introduced by MacIntyre when first broadcast as the saddest story he ever had to tell. Winner of an Anik Award, it was removed from competition at the Cannes Film Festival and banned in Canada for several years due to court orders on behalf of some of the subjects.
• "His Word Against History: The Stephen Truscott Story" (2000). It was a co-recipient (with other fifth estate documentaries) of the Michener Award for meritorious public service journalism.
• "The Scandal of the Century" (2001) about false accusations of sexual abuse in Saskatchewan (see Sheila Steele).
• "Terror and Tehran" (2002) about US policy in Iran. Transcript of an online discussion about the program from the Washington Post)
• "Toxic Company" (with Frontline and New York Times Television, 2003). An expose of McWane, it won a Dupont/Columbia Silver Baton, the George Polk Award, the George Foster Peabody Award and the CBC's Wilderness award. The accompanying New York Times series, "Dangerous Business", won a Pulitzer Prize.
• "A Hail of Bullets" (2005) about the Mayerthorpe incident.
• "Brian Mulroney: The Unauthorized Chapter" (2007) about the Airbus affair.

During a fifty-day lockout by the CBC in 2005, MacIntyre penned a memoir called Causeway: A Passage from Innocence, which he dedicated to his mother. He has five children including CBC reporter Darrow MacIntyre. He married broadcaster Carol Off in 2000.

Novels

• The Long Stretch, 1999
• The Bishop's Man, 2009 - Winner of the 2009 Scotiabank Giller Prize - Winner of the 2010 Libris Fiction Book of the Year Award.

Non-fiction

• Who Killed Ty Conn (with Theresa Burke), 2001 (updated edition announced for 2011)
• Causeway: A Passage from Innocence, 2006