Mackay, who played professionally for Zimbabwe, has 17 years of experience in sport and business management.
Malcolm Cannon resigned in July after four years in the post.
“These are exciting times for everyone involved in our great game in Scotland,” said Mackay, whose grandparents are both from Scotland.
“I have been impressed with the clear vision, strategy and more importantly, commitment of the board to achieve full member status of the International Cricket Council.
“This will help us achieve our vision to make cricket mainstream in Scotland and thereby ensure the long term sustainability of the game.”
Mackay, 52, was formerly the chief executive of Sussex County Cricket Club as well as CEO of Harlequins RL and managing director of worcester warriors.
Last month, Scotland came second in a Twenty20 tri-series with Ireland and Netherlands, a warm-up for the T20 World Cup Qualifier which starts United Arab Emirates on 11 October.
Cricket Scotland chair Tony Brian added: “We are currently finalising an ambitious strategy which aims to make cricket one of the mainstream sports in Scotland over the next 10 years, with a wide increase in participation to sees us becoming a Full Member of the International Cricket Council within the next five.
“Gus’s proven skills as a leader of sports bodies and his wide network of contacts throughout the cricketing world make him the ideal person to lead cricket in Scotland through the next, and exciting, phase of our development.”