| Tuesday 10th August 1999 | |||
| First Round | |||
| Airdrieonians | 2-1 | Dumbarton | |
| Arbroath | 3-2 | East Fife | |
| Ayr United | 0-1 | Raith Rovers | |
| Berwick Rangers | 4-1 | Queen of the South | |
| Brechin City | 0-1 | Queen's Park | |
| Clyde | 0-4 | Ross County | |
| Cowdenbeath | 0-4 | Alloa Athletic | |
| Dunfermline Athletic | 2-2 | Morton | aet |
| (Morton won on penalties) | |||
| East Stirlingshire | 1-2 | Clydebank | aet |
| Inverness CT | 1-0 | St Mirren | |
| Montrose | 1-3 | Hamilton Academical | |
| Partick Thistle | 0-2 | Albion Rovers | |
| Stirling Albion | 2-2 | Stenhousemuir | aet |
| (Stirling Albion won on penalties) | |||
| Stranraer | 2-2 | Partick Thistle | aet |
| (Stranraer won on penalties) | |||
» Scottish Challenge Cup 1999-2000 : Results
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