Clarke has been lured to the position by the NBA Global Academy after becoming an integral part of Saint Mary's College in California over the past five years.
He previously spent 12 years with the AIS and a number of Aussies that progressed through the program including Patty Mills, Matthew Dellavedova, Andrew Bogut, Joe Ingles and Ben Simmons have all validated Clarke's ability to identify, nurture, and develop athletes with that elusive thing known as 'potential.'
"I am excited about the opportunity to further establish and grow a program that will help develop young players with outstanding potential from all parts of the world," said Clarke.
"It will be an honor to work for an organisation as professional as the NBA and with one as passionate as Basketball Australia.
"The chance to interact with coaches from many different backgrounds and levels is also appealing.
"I am very much looking forward to watching the individuals develop and mature, create a solid foundation and set the bar high for groups that follow."
"One of the main priorities of the NBA Global Academy is preparing athletes for the college system," said General Manager High Performance, Jan Stirling.
"Marty is highly respected in that same US college system due to the positive impact he has delivered at Saint Mary's and the Global Academy's choice to select him as director is one that Basketball Australia highly endorses."