Glasgow Perthshire, Harthill Royal, and Livingston United did not compete, along with Aberdeen University who also withdrew from their league and Syngenta who had folded.
Defending champions Cumnock Juniors were eliminated in the second round by local rivals Auchinleck Talbot.
The dates for each round of the 2023–24 tournament were as follows: Drawn matches proceed direct to a penalty shootout, with no extra time.
The 15 clubs taking part in the Scottish Cup — Auchinleck Talbot, Beith Juniors, Benburb, Camelon Juniors, Carluke Rovers, Carnoustie Panmure, Culter, Cumnock Juniors, Darvel, Glenafton Athletic, Irvine Meadow XI, Lochee United, Pollok, Rutherglen Glencairn, and Tayport — received a bye into the second round draw along with St Anthony's.
The Final of the Scottish Junior Cup was played at Broadwood Stadium, Cumbernauld on Sunday 2 June with a 4.05pm kick off.