The Bruntsfield Links player carded an eagle and ten birdies as he fired an eight-under-par 64 on the Rosemount course at the Perthshire venue.
The brilliant effort, which saw him come home in 30, seven-under, left McIntosh three shots clear of the field heading into the final stroke-play round.
The top 64 after that progress to a match-play segment and McIntosh has already shown his liking for that format when winning the Scottish Boys’ Championship at Murcar Links in 2016.
Lundin’s Andrew Thornton and Charleton’s Andrew Davidson were next best among those starting out on Rosemount with 67s.
Sean Marc (Broomieknowe), Royal Musselburgh’s Stuart Blair, Michael Brodie of Alyth and Kyle Godsman (Moray) shared pride of place on the Lansdowne course with three-under-par 69s.
On the Tartan Tour, Greig Hutcheon has a sixth Emtec Group Deer Park Masters title triumph in his sights after firing an opening 67 at the Livingston venue. The five-under-par effort earned Hutcheon, who is attached to the Paul Lawrie Golf Centre, a two-shot lead over Paul O’Hara (North Lanarkshire Leisure Ltd).
Chris Currie (Erskine) and Gareth Wright (West Linton) are a shot further back in joint-third but defending champion Gavin Hay (Mearns Castle) had to settle for a 74.