A total of 129 clubs entered the competition, which was 28 fewer than the previous season. This was due to 25 teams leaving the Junior ranks for the East of Scotland League along with Cruden Bay, Inverness City, and Lewis United not entering the tournament.
Auchinleck Talbot were the defending champions. They successfully defended their title with a 2–0 win over Largs Thistle in the final.
Drawn matches are replayed and replays that end in a draw proceed direct to a penalty shootout, there is no extra time. Semi-finals are played home and away over two legs with the winner on aggregate progressing to the final. If the aggregate score is tied at the end of the second leg, the match will also proceed direct to a penalty shootout.
Also qualified automatically for the second round were Banks O'Dee, who achieved national club licensing requirements, and Girvan, who qualify automatically as historic full members of the Scottish Football Association.
The first and second round draws took place at Hampden Park, Glasgow on 23 August 2018.
1 Tie awarded to Cumnock Juniors as Coupar Angus unable to raise side.[2] 2 Tie played at Victoria Park, Newmains after Rosyth's Fleet Grounds deemed unsuitable to host match.[3] 3 Tie played at Valefield Park, Kilbirnie after Gartcairn's MTC Park deemed unsuitable to host match.[4]
The Final of the Macron Scottish Junior Cup was played at New Douglas Park, Hamilton on Sunday 2 June with a 4.10pm kick off. The game was televised live by BBC Alba. Both teams wore their away strips.
