Mr Urquhart will be succeeded by chief operating officer Ewen Mackintosh, who will become the first non-family member to run the company.
The change comes after Michael's brother, David Urquhart, stepped down as joint managing director in 2012. The brothers, who had run the business together since 2007, belong to the third generation of the owning Urquhart family.
Five members of the fourth generation are employed at the business, which launched the Benromach Distillery in 1998 after acquiring it in 1993.
Michael Urquhart joined Gordon & MacPhail as finance director in 1981 after qualifying as a chartered accountant. He said: "After 33 years - most of my working life - with Gordon & MacPhail - it is time to hand on the reins. It is gratifying to be able to do so at a time of such strong, sustained growth in the company.
"I'm particularly pleased that I will be succeeded by Ewen, who has been an instrumental figure in the company since 1991.
"He is a very safe pair of hands and it will very much be business as usual for Gordon & MacPhail."