Born on the Isle of Mull in the Inner Hebrides in Scotland, he attended school in Oban, followed by the University of Edinburgh and Moray House School of Education. He joined BBC Scotland as a researcher in 1975.
He became a radio producer for BBC Highland then transferred as a producer in Television in 1979. He was instrumental in introducing daily Gaelic children's programmes on BBC Scotland and developed the investigative current affairs programmes Prosbaig, Eòrpa and the children's programme Dè a-nis?.
In 1992 he became Head of Gaelic and Features and of Children's. By 2000 he had become Head of Programmes which gave him responsibility for production and commissioning of all BBC Scotland output. He was appointed Controller of BBC Scotland in April 2004.
As a senior member of the BBC Editorial Standards Committee, MacQuarrie has twice been asked to investigate high-profile incidents in the BBC. His 2012 report into Newsnight (following the programme wrongly accusing Lord McAlpine of abusing care-home boys) led to widespread changes in editorial policy. MacQuarrie was later commissioned by Director General Tony Hall to investigate Jeremy Clarkson's assault on his Top Gear producer.
- "Ken MacQuarrie, Director, Nations and Regions". Inside the BBC. Retrieved 23 April 2017. CS1 maint: discouraged parameter (link)
- "BBC Scotland head Ken MacQuarrie given new UK-wide director role". BBC News. 22 September 2016.
- "Ken MacQuarrie profile". Royal Television Society. Retrieved 23 April 2017. CS1 maint: discouraged parameter (link)
- "Ken MacQuarrie report: Summary of findings". BBC News. 12 November 2012.
- "BBC Director-General's statement regarding Jeremy Clarkson". BBC Media Centre. 25 March 2015.
- "BBC Board and Executive". Inside the BBC. Retrieved 23 April 2017. CS1 maint: discouraged parameter (link)