Auto Windscreens Shield 1998-99 
Winners: Wigan Athletic Runners-up: Millwall Winners from previous season: Grimsby Town First round
| Northern section | Carlisle United, Chesterfield, Halifax Town, Lincoln City, Rochdale, Scarborough, Scunthorpe United and York City given byes to the second round. | | 8 December 1998 | Blackpool | 0 | - | 2 | Stoke City | 1,759 | Bloomfield Road, Blackpool | | 8 December 1998 | Burnley | 0 | - | 1 | Preston North End | 3,366 | Turf Moor, Burnley | | 8 December 1998 | Macclesfield Town | 0 | - | 1 | Wrexham | 804 | Moss Rose, Macclesfield | | 8 December 1998 | Chester City | 1 | - | 2 | Hartlepool United (won on sudden death extra time by golden goal) | 960 | Deva Stadium, Chester (aet) | | 8 December 1998 | Manchester City | 1 | - | 2 | Mansfield Town | 3,007 | Maine Road, Manchester | | 8 December 1998 | Oldham Athletic | 0 | - | 1 | Darlington (won on sudden death extra time by golden goal) | 2,133 | Boundary Park, Oldham (aet) | | 8 December 1998 | Rotherham United | 0 | - | 3 | Wigan Athletic | 1,225 | Millmoor, Rotherham | | 22 December 1998 | Notts County | 0 | - | 1 | Hull City | 1,109 | Meadow Lane, Nottingham | Southern Section
| Brighton & Hove Albion, Cambridge United, Exeter City, Fulham, Luton Town, Northampton Town, Southend United and Torquay United given byes to the second round. | | 5 December 1998 | Colchester United | 1 | - | 5 | Gillingham | 1,742 | Layer Road, Colchester | | 8 December 1998 | AFC Bournemouth | 2 | - | 0 | Reading | 2,666 | Dean Court, Bournemouth | | 8 December 1998 | Brentford | 2 | - | 0 | Plymouth Argyle | 1,580 | Griffin Park, London | | 8 December 1998 | Peterborough United | 3 | - | 0 | Leyton Orient | 1,801 | London Road, Peterborough | | 8 December 1998 | Shrewsbury Town | 0 | - | 1 | Wycombe Wanderers (won on sudden death extra time by golden goal) | 1,033 | Gay Meadow, Shrewsbury (aet) | | 8 December 1998 | Swansea City | 4 | - | 1 | Barnet | 1,017 | Vetch Field, Swansea | | 8 December 1998 | Walsall (won 5-4 on pens.) | 2 | - | 2 | Bristol Rovers | 2,210 | Bescot Stadium, Walsall (aet) | 9 December 1998 | Millwall | 2 | - | 0 | Cardiff City | 1,858 | The New Den, London | Second round | Northern section | | 5 January 1999 | Halifax Town | 4 | - | 2 | York City | 1,446 | The Shay, Halifax | | 5 January 1999 | Hull City | 1 | - | 2 | Wrexham | 2,331 | Boothferry Park, Kingston-upon-Hull | | 5 January 1999 | Lincoln City | 1 | - | 0 | Mansfield Town | 2,289 | Sincil Bank, Lincoln | | 12 January 1999 | Darlington | 0 | - | 2 | Chesterfield | 1,391 | Feethams, Darlington | | 19 January 1999 | Hartlepool United (won 4-3 on pens.) | 2 | - | 2 | Preston North End | 1,205 | Victoria Park, Hartlepool (aet) | | 19 January 1999 | Scunthorpe United | 1 | - | 1 | Carlisle United (won 4-3 on pens.) | 1,507 | Glanford Park, Scunthorpe (aet) | | 19 January 1999 | Wigan Athletic | 3 | - | 0 | Scarborough | 1,693 | Springfield Park, Wigan | | 2 February 1999 | Stoke City | 1 | - | 2 | Rochdale | 7,361 | Brittania Stadium, Stoke | Southern section | | 5 January 1999 | AFC Bournemouth | 5 | - | 1 | Peterborough United | 3,398 | Dean Court, Bournemouth | | 5 January 1999 | Brighton & Hove Albion | 1 | - | 5 | Milwall | 2,003 | Priestfield, Gillingham | | 5 January 1999 | Cambridge United | 3 | - | 2 | Northampton Town | 2,391 | Abbey Stadium, Cambridge | | 5 January 1999 | Exeter City | 3 | - | 1 | Southend United | 1,143 | St James's Park, Exeter | | 5 January 1999 | Luton Town | 0 | - | 3 | Walsall | 1,870 | Kenilworth Road, Luton | | 5 January 1999 | Swansea City | 0 | - | 1 | Gillingham | 5,126 | Vetch Field, Swansea | | 5 January 1999 | Torquay United (won on sudden death extra time by golden goal) | 2 | - | 1 | Fulham | 2,596 | Plainmoor, Torquay (aet) | | 5 January 1999 | Wycombe Wanderers | 1 | - | 4 | Brentford | 2,010 | Adams Park, High Wycombe | | Quarter-finals | | Northern section | | 19 January 1999 | Wrexham | 3 | - | 2 | Chesterfield | 1,572 | Racecourse Ground, Wrexham | | 26 January 1999 | Carlisle United | 0 | - | 3 | Wigan Athletic | 2,383 | Brunton Park, Carlisle | | 26 January 1999 | Hartlepool United | 0 | - | 3 | Lincoln City | 1,370 | Victoria Park, Hartlepool | | 23 February 1999 | Rochdale (won on sudden death extra time by golden goal) | 2 | - | 1 | Halifax Town | 2,327 | The Shay, Halifax (aet) (match switched to The Shay due to problems with pitch at Spotland) | Southern section | | 19 January 1999 | Brentford | 0 | - | 0 | Walsall (won 5-4 on pens.) | 2,048 | Griffin Park, London (aet) | | 19 January 1999 | Cambridge United (won 5-3 on pens.) | 1 | - | 1 | Exeter City | 2,758 | Abbey Stadium, Cambridge (aet) | | 23 January 1999 | Torquay United | 0 | - | 1 | Gillingham | 3,121 | Plainmoor, Torquay | | 2 February 1999 | AFC Bournemouth | 1 | - | 1 | Millwall (won 4-3 on pens.) | 5,339 | Dean Court, Bournemouth (aet) | Semi-Finals | Northern section | | 16 February 1999 | Lincoln City | 1 | - | 2 | Wrexham (won on sudden death extra time by golden goal) | 3,490 | Sincil Bank, Lincoln (aet) | | 8 March 1999 | Rochdale | 0 | - | 2 | Wigan Athletic | 2,484 | Spotland, Rochdale | Southern section | | 16 February 1999 | Millwall (won on sudden death extra time by golden goal) | 1 | - | 0 | Gillingham | 11,555 | The New Den, London (aet) | | 16 February 1999 | Walsall (won 4-3 on pens.) | 1 | - | 1 | Cambridge United | 5,087 | Bescot Stadium, Walsall (aet) | Area Finals | Northern section: 1st leg | | 16 March 1999 | Wigan Athletic | 2 | - | 0 | Wrexham | 4,938 | Springfield Park, Wigan | | Southern section: 1st leg | | 9 March 1999 | Millwall | 1 | - | 0 | Walsall | 11,626 | The New Den, London | | Northern section: 2nd leg | | 23 March 1999 | Wrexham | 2 | - | 3 | Wigan Athletic | 4,941 | Racecourse Ground, Wrexham | | (Wigan Athletic win 5-2 on aggregate) | Southern section: 2nd leg | | 16 March 1999 | Walsall | 1 | - | 1 | Millwall | 9,158 | Bescot Stadium, Walsall | (Millwall win 2-1 on aggregate) | National final | | 18 April 1999 | Wigan Athletic | 1 | - | 0 | Millwall | 55,349 | Wembley Stadium, London |
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