Football League Fourth Division 1988/89
| Pos | Club | Pld | W | D | L | F | A | GD | Pts | Notes |
| 1st | Rotherham United | 46 | 22 | 16 | 8 | 76 | 35 | +41 | 82 | ▲Champions |
| 2nd | Tranmere Rovers | 46 | 21 | 17 | 8 | 62 | 43 | +19 | 80 | ▲Runners Up |
| 3rd | Crewe Alexandra | 46 | 21 | 15 | 10 | 67 | 48 | +19 | 78 | ▲Promoted |
| 4th | Scunthorpe United | 46 | 21 | 14 | 11 | 77 | 57 | +20 | 77 | ♦Playoffs |
| 5th | Scarborough | 46 | 21 | 14 | 11 | 67 | 52 | +15 | 77 | ♦Playoffs |
| 6th | Leyton Orient | 46 | 21 | 12 | 13 | 86 | 50 | +36 | 75 | ♦▲PO Winners |
| 7th | Wrexham | 46 | 19 | 14 | 13 | 77 | 63 | +14 | 71 | ♦Playoffs |
| 8th | Cambridge United | 46 | 18 | 14 | 14 | 71 | 62 | +9 | 68 | - |
| 9th | Grimsby Town | 46 | 17 | 15 | 14 | 65 | 59 | +6 | 66 | - |
| 10th | Lincoln City | 46 | 18 | 10 | 18 | 64 | 60 | +4 | 64 | - |
| 11th | York City | 46 | 17 | 13 | 16 | 62 | 63 | -1 | 64 | - |
| 12th | Carlisle United | 46 | 15 | 15 | 16 | 53 | 52 | +1 | 60 | - |
| 13th | Exeter City | 46 | 18 | 6 | 22 | 65 | 68 | -3 | 60 | - |
| 14th | Torquay United | 46 | 17 | 8 | 21 | 45 | 60 | -15 | 59 | - |
| 15th | Hereford United | 46 | 14 | 16 | 16 | 66 | 72 | -6 | 58 | - |
| 16th | Burnley | 46 | 14 | 13 | 19 | 52 | 61 | -9 | 55 | - |
| 17th | Peterborough United | 46 | 14 | 12 | 20 | 52 | 74 | -22 | 54 | - |
| 18th | Rochdale | 46 | 13 | 14 | 19 | 56 | 82 | -26 | 53 | - |
| 19th | Hartlepool United | 46 | 14 | 10 | 22 | 50 | 78 | -28 | 52 | - |
| 20th | Stockport County | 46 | 10 | 21 | 15 | 54 | 52 | +2 | 51 | - |
| 21st | Halifax Town | 46 | 13 | 11 | 22 | 69 | 75 | -6 | 50 | - |
| 22nd | Colchester United | 46 | 12 | 14 | 20 | 60 | 78 | -18 | 50 | - |
| 23rd | Doncaster Rovers | 46 | 13 | 10 | 23 | 49 | 78 | -29 | 49 | - |
| 24th | Darlington | 46 | 8 | 18 | 20 | 53 | 76 | -23 | 42 | ▼Relegated |
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Football League Third Division/Fourth Division - The Playoffs |
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Semi Finals 1st Leg |
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| Date | Home | Score | Away |
| Sun May 21 | Leyton Orient | 2-0 | Scarborough |
| Sun May 21 | Wrexham | 3-1 | Scunthorpe United |
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Semi Finals 2nd Leg |
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| Wed May 24 | Scarborough | 1-0 | Leyton Orient |
| Leyton Orient Won 2-1 on aggregate | |||
| Wed May 24 | Scunthorpe United | 0-2 | Wrexham |
| Wrexham Won 2-0 on aggregate | |||
| Final 1st Leg | |||
| Tue May 30 | Wrexham | 0-0 | Leyton Orient |
| Final 2nd Leg | |||
| Sat June 3 | Leyton Orient | 2-1 | Wrexham |
| Leyton Orient Won 2-1 on aggregate | |||
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End of Season Notes |
| ▼Southend United were Relegated from the Third Division |
| ▼Chesterfield were Relegated from the Third Division |
| ▼Gillingham were Relegated from the Third Division |
| ▼Aldershot were Relegated from the Third Division |
| ▲Rotherham United were Promoted to the Third Division |
| ▲Tranmere Rovers were Promoted to the Third Division |
| ▲Crewe Alexandra were Promoted to the Third Division |
| ♦ Scunthorpe United Qualified for the Playoffs |
| ♦ Scarborough Qualified for the Playoffs |
| ♦ Leyton Orient Qualified for the Playoffs |
| ♦ Wrexham Qualified for the Playoffs |
| ▲Leyton Orient were Promoted to the Third Division via the Playoffs |
| ▼Darlington were automatically Relegated to the Conference after finishing bottom of the Football League |
| ▲Maidstone United were Promoted from the Football Conference |