It will include three programmes - elite, development and golf activities - and follows the success of Scotland's first Tennis Academy (in partnership with St George's School for Girls and Tennis Scotland) being established at Merchiston in 2007.
"At Merchiston we have experience of dealing with gifted and talented children in all areas of life, including international sports players," said headmaster Andrew Hunter.
"The Golf Academy is a wonderful opportunity to keep Scottish (and indeed UK) talent in the UK, and to provide an environment for these players, in which they will receive an excellent education, can be around friends of their own age, and access a top-class golf programme."
Coaching will take place at the Kings Acre Golf Academy, where Murdoch, a highly- respected coach, is the director of golf.
He will be assisted by Ian Butcher, who has been based at the well-equipped Lasswade facility for the past few years and also has an excellent reputation in coaching circles.
Both Murdoch and Butcher will work with Merchiston's director of sport, Richard Charman, to ensure that each boy's training and educational needs are met, and that progress is tracked to ensure that the appropriate standards are being achieved.
According to one of Butch Harmon's former assistants, the new Academy couldn't be in safer hands. "Merchiston's Golf Academy couldn't have two better instructors in Alan and Ian," said Shawn Callaghan, who worked with the American for five years.
"Their passion for and knowledge of the game is impressive. The facility at Kings Acre is as good as anything I have seen in the United States."
The first admissions to the new Golf Academy will be in September.