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