| Tournament details | |
|---|---|
| Country |  Scotland |
| Teams | 163 |
| Defending champions | Kilwinning Rangers |
| Final positions | |
| Champions | Whitburn |
| Runner-up | Johnstone Burgh |
| Tournament statistics | |
| Matches played | 162 (not including replays) |
The 1999–2000 Scottish Junior Cup was a competition in Scottish Junior football. It was won by Whitburn; they defeated Johnstone Burgh 4–3 on penalties after drawing 2–2 in the final.
First round
These ties were scheduled to take place on Saturday 9 October 1999.
| Home Team | Score | Away Team |
|---|---|---|
Second round
These ties were scheduled to take place on Saturday 6 November 1999.
| Home Team | Score | Away Team |
|---|---|---|
Third round
These ties were scheduled to take place on Saturday, 4 December 1999
| Home Team | Score | Away Team |
|---|---|---|
Fourth round
These ties were scheduled to take place on Saturday, 15 January 2000.
| Home Team | Score | Away Team |
|---|---|---|
Fifth round
These ties were scheduled to take place on Saturday, 12 February 2000.
| Home Team | Score | Away Team |
|---|---|---|
| Benburb | 3 – 0 | Larkhall Thistle |
| Cumnock Juniors | 3 – 0 | Kilbirnie Ladeside |
| Johnstone Burgh | 2 – 1 | Glenafton Athletic |
| Lanark United | 2 – 0 | Thornton Hibs |
| Maybole Juniors | 3 – 0 | Arbroath Sporting Club |
| Neilston | 2 – 3 | Whitburn |
| Newtongrange Star | 2 – 0 | Sunnybank |
| Shotts Bon Accord | 2 – 2 | Carnoustie Panmure |
| replay | 2 – 1 |
Quarter finals
These ties were played on Saturday 11 March 2000.
| Home Team | Score | Away Team |
|---|---|---|
| Benburb | 2 – 1 | Newtongrange Star |
| Johnstone Burgh | 2 – 1 | Cumnock Juniors |
| Lanark United | 0 – 2 | Shotts Bon Accord |
| Whitburn | 3 – 1 | Arbroath Sporting Club |
Semi-finals
These ties were played on 28 April 2000 & 5 May 2000, respectively.
| Home Team | Score | Away Team | Venue |
|---|---|---|---|
| Benburb | 1 – 1 | Whitburn | |
| Johnstone Burgh | 2 – 2 | Shotts Bon Accord |
Final
The final took place on Sunday 28 May 2000.
| Home Team | Score | Away Team | Venue |
|---|---|---|---|
| Whitburn | 2 – 2 | Johnstone Burgh | Firhill Stadium, Partick Thistle |
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