The former Cove Rangers chairman was chosen to replace Campbell Ogilvie at the governing body’s annual general meeting at Hampden. Rod Petrie was re-elected as vice-president.
McRae will now head up the SFA’s eight-man board and will represent the governing body at FIFA and UEFA meetings.
He will also play a leading role in the appointment process if chief executive Stewart Regan or Scotland boss Gordon Strachan require to be replaced.
A former Cove player who signed for the club in 1979, the construction firm owner eventually swapped the dressing room for the boardroom when he was appointed one of the Aberdeenshire outfit’s directors.
Within five years of taking charge of the Allan Park side, he had led the club from the amateur ranks to the Highland League.
As well as serving as the Highland League’s president, he has also been involved with the SFA since 1993.
He steps up to become SFA president after two spells as vice-president having previously helped hire former Scotland managers George Burley and Craig Levein.
Ogilvie, who served as Rangers secretary for 27 years before moving to Hearts in 2005 where he was appointed operations director, now steps down.
He replaced George Peat as SFA president in 2011 before presiding over the re-organisation of Scotland’s league set-up in 2013.
The Scottish Football League and Scottish Premier League merged to form the Scottish Professional Football League.
A play-off system was introduced for the top-flight, while a pyramid set-up handed Highland League clubs and teams from the newly-formed Lowland League an opportunity to play their way into the senior ranks.