| Tournament details | |
|---|---|
| Country | Scotland | 
| Defending champions | Auchinleck Talbot | 
| Final positions | |
| Champions | Linlithgow Rose | 
| Runner-up | Kelty Hearts | 
The 2006–07 Scottish Junior Cup was a competition in Scottish Junior football. It was won for the third time by Linlithgow Rose after they defeated Kelty Hearts 2–1 in the final.
Under a new rule change, the Junior Cup winners (along with winners of the North, East and West regional leagues) qualify for the senior Scottish Cup; Linlithgow Rose therefore competed in the 2007–08 Scottish Cup.
First round
These ties were scheduled to take place on Saturday 30 September 2006.
Replays
| Home Team | Score | Away Team | 
|---|---|---|
| Neilston Juniors | 1 – 2 | Cambuslang Rangers | 
| Saltcoats Victoria | 0 – 2 | Culter | 
| Dalkeith Thistle | 2 – 3 | Glasgow Perthshire | 
Second round
These ties were scheduled to take place on Saturday 4 November 2006.
Replays
| Home Team | Score | Away Team | 
|---|---|---|
| Lanark United | 2 – 1 | Glenafton Athletic | 
| Newmains United | 4 – 3 | Hurlford United | 
| Kello Rovers | 1 – 4 | Longside | 
| Musselburgh Athletic | 2 – 1 | Downfield | 
| East Craigie | 2 – 1 | Buchanhaven Hearts | 
| Banchory St. Ternan | 0 – 1 | Montrose Roselea | 
| Bathgate Thistle | 2 – 3 | Carnoustie Panmure | 
| Glenrothes | 0 – 3 | Bellshill Athletic | 
| Faulhouse United | 0 – 0 (4 – 2 pen.)  | 
Cumbernauld United | 
| Craigmark Burntonians | 0 – 4 | Banks O' Dee | 
| Blairgowrie | 1 – 2 | Petershill | 
Third round
These ties were scheduled to take place on Saturday, 2 December 2006.
Replays
| Home Team | Score | Away Team | 
|---|---|---|
| Broughty Athletic | 2 – 1 | Fauldhouse United | 
| Hill of Beath Hawthorn | 2 – 4 | Bellshill Athletic | 
| Kelty Hearts | 3 – 2 | Whitburn | 
| Kilsyth Rangers | 1 – 0 | Blackburn United | 
| Kilwinning Rangers | 2 – 1 | Lugar Boswell Thistle | 
| Renfrew | 4 – 0 | Hermes | 
Fourth round
These ties were scheduled to take place on Saturday 13 January 2007.
| Home Team | Score | Away Team | 
|---|---|---|
| Arbroath Victoria | 0 – 5 | Kilsyth Rangers | 
| Broughty Athletic | 2 – 6 | Kelty Hearts | 
| Tranent | 1 – 0 | Banks O' Dee | 
| Lanark United | 1 – 1 | Bellshill Athletic | 
| replay | 1 – 1 (5 – 3p) | |
| Aberdeen East End | 0 – 4 | Linlithgow Rose | 
| Auchinleck Talbot | 3 – 3 | Lochee United | 
| replay | 0 – 0 (3 – 4p) | |
| Lochee Harp | 3 – 3 | Irvine Meadow XI | 
| replay | 0 – 5 | |
| East Kilbride Thistle | 3 – 0 | Irvine Victoria | 
| Ballingry Rovers | 1 – 1 | Petershill | 
| replay | 0 – 1 | |
| Kilwinning Rangers | 1 – 1 | Rutherglen Glencairn | 
| replay | 1 – 0 | |
| Yoker Athletic | 1 – 1 | Ellon United | 
| replay | 1 – 0 | |
| Pollok | 4 – 1 | Kinnoull | 
| Renfrew | 0 – 5 | Arthurlie | 
| Neilston Juniors | 1 – 1 | Bonnyrigg Rose Athletic | 
| replay | 3 – 0 | |
| Musselburgh Athletic | 3 – 0 | Dundonald Bluebell | 
Replays
| Home Team | Score | Away Team | 
|---|---|---|
Fifth round
These ties were scheduled to take place on Saturday 10 February 2007.
| Home Team | Score | Away Team | 
|---|---|---|
| Lochee United | 1 – 3 | Linlithgow Rose | 
| Lanark United | 2 – 0 | East Kilbride Thistle | 
| Arthurlie | 1 – 1 | Petershill | 
| replay | 5 – 1 | |
| Yoker Athletic | 2 – 2 | Tranent | 
| replay | 2 – 0 | |
| Neilston Juniors | 1 – 1 | Musselburgh Athletic | 
| replay | 2 – 0 | |
| Kilwinning Rangers | 1 – 1 | Camelon | 
| replay | 2 – 0 | |
| Kelty Hearts | 2 – 1 | Kilsyth Rangers | 
| Irvine Meadow XI | 1 – 1 | Pollok | 
| replay | 1 – 2 | 
Quarter finals
These ties were played on Saturday 10 March 2007.
| Home Team | Score | Away Team | 
|---|---|---|
| Neilston Juniors | 1 – 2 | Kilwinning Rangers | 
| Arthurlie | 4 – 2 | Yoker Athletic | 
| Lanark United | 0 – 1 | Kelty Hearts | 
| Linlithgow Rose | 1 – 0 | Pollok | 
Semi-finals
These ties were played on 13 April and 20 April, respectively.
| Home Team | Score | Away Team | Venue | 
|---|---|---|---|
| Arthurlie | 1 – 4 | Linlithgow Rose | Love street, Paisley | 
| Kelty Hearts | 3 – 0 | Kilwinning Rangers | New Douglas Park, Hamilton | 
Final
The final took place on 3 June 2007.
| Home Team | Score | Away Team | Venue | 
|---|---|---|---|
| Kelty Hearts | 1 – 2 | Linlithgow Rose | East End Park, Dunfermline |