In 2004, Embry was hired to be the senior basketball advisor to Rob Babcock, the rookie general manager for the Toronto Raptors. After one season, Embry was elevated from senior advisor to president, bypassing Babcock in the chain of command when the board cited a lack of confidence in Babcock's moves. On January 26, 2006, Embry was named the interim general manager for the Raptors after the firing of Babcock, a position he held for two months until Bryan Colangelo was hired as the general manager. Embry has continued to serve as senior basketball advisor for the Raptors. Since then, the Raptors went on to become NBA champions in 2019.