In a keenly-fought contest on the Capital course, the East Lothian youngster pipped Bathgate’s Greg Millar in a card play-off.
Both players shot commendable 74s in the blustery conditions but Blair’s better back nine saw him claim the spoils.
A countback was also required to determine the minor placings after four players posted 75s.
Douglas Imrie (Royal Burgess) took third spot ahead of Bruntsfield Links’ Ross Brydon by virtue of a better last hole, with Mark Napier (Dundas Parks) and Aoden Donnelly (Murrayfield) next on the scoreboard.
Napier claimed the top handicap prize with a net 68, beating five-handicapper Donnelly by two shots.
Lothians Boys Champion of Champions (at Torphin Hill): 74 Stuart Blair (Royal Musselburgh), Greg Millar (Bathgate). 75 Douglas Imrie (Royal Burgess), Ross Brydon (Bruntsfield Links), Mark Napier (Dundas Parks), Aoden Donnelly (Murrayfield). 76 Andrew Young (BBT), Nathan Free (Musselburgh Old). 77 Connor Scott (Duddingston), Calum Cochrane (Marriott Dalmahoy). 78 Lewis Fenn (Castle Park), Scott Finlay (Liberton). 79 Kyle Brown (Swanston New), Sean Walter (Dunbar & West Linton), Calum Burgess (Musselburgh). 80 Ross Millar (Whitekirk) Euan Bowden (Glen), Gregor Drummond (Ratho Park). 81 Thomas Grant (Kingsknowe), Jordan West (Uphall), Greg Thorburn (Newbattle), Fraser Christie (Craigmillar Park), Calum Hill (Tantallon).