Former Manchester United and Scotland striker McClair joins the SFA after 13 years on the coaching staff at Old Trafford.
McClair replaces Mark Wotte who left his role as performance director with the SFA in October last year.
McClair, 51, leaves his post as director of Man Utd’s youth academy, and will start with the SFA on June 1.
The SFA say McClair was “identified unanimously as the preferred candidate” during a recruitment process which involved Scotland coach Gordon Strachan as well as former Scotland bosses Walter Smith and Andy Roxburgh.
McClair said: “I am extremely proud to have been given the responsibility to help Scottish football move forward.
???I am sure my experiences can be of benefit to Scottish football and, having spent the majority of the last 30 years in England with Manchester United, I am looking forward to coming home.”