Football League Second Division 1898/99
| Pos | Club | Pld | W | D | L | F | A | GA | Pts | Notes |
| 1st | Manchester City | 34 | 23 | 6 | 5 | 92 | 35 | 2.629 | 52 | ▲Champions |
| 2nd | Glossop North End | 34 | 20 | 6 | 8 | 76 | 38 | 2.000 | 46 | ▲Runners Up |
| 3rd | Leicester Fosse | 34 | 18 | 9 | 7 | 64 | 42 | 1.524 | 45 | - |
| 4th |  Newton
Heath |
34 | 19 | 5 | 10 | 67 | 43 | 1.558 | 43 | - |
| 5th | New Brighton Tower | 34 | 18 | 7 | 9 | 71 | 52 | 1.365 | 43 | - |
| 6th | Walsall | 34 | 15 | 12 | 7 | 79 | 36 | 2.194 | 42 | - |
| 7th | Woolwich Arsenal | 34 | 18 | 5 | 11 | 72 | 41 | 1.756 | 41 | - |
| 8th | Small Heath | 34 | 17 | 7 | 10 | 85 | 50 | 1.700 | 41 | - |
| 9th | Burslem Port Vale | 34 | 17 | 5 | 12 | 56 | 34 | 1.647 | 39 | - |
| 10th | Grimsby Town | 34 | 15 | 5 | 14 | 71 | 60 | 1.183 | 35 | - |
| 11th | Barnsley | 34 | 12 | 7 | 15 | 51 | 56 | 0.929 | 31 | - |
| 12th | Lincoln City | 34 | 12 | 7 | 15 | 51 | 56 | 0.911 | 31 | - |
| 13th | Burton Swifts | 34 | 10 | 8 | 16 | 51 | 70 | 0.729 | 28 | - |
| 14th | Gainsborough Trinity | 34 | 10 | 5 | 19 | 56 | 72 | 0.778 | 25 | - |
| 15th | Luton Town | 34 | 10 | 3 | 21 | 51 | 95 | 0.537 | 23 | - |
| 16th | Blackpool | 34 | 8 | 4 | 22 | 49 | 90 | 0.544 | 20 | ▼Not Re Elected |
| 17th | Loughborough | 34 | 6 | 6 | 22 | 38 | 92 | 0.413 | 18 | Re Elected |
| 18th | Darwen | 34 | 2 | 5 | 27 | 22 | 141 | 0.156 | 9 | ▼Resigned |
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Election for League Membership |
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| Darwen did not seek Re-Election so the other bottom two clubs were required to seek re-election to the League. They were joined in the vote for League membership by 7 non-league clubs. | ||
| Votes | Club | End Result |
| 28 | Loughborough | Re Elected to the League |
| 17 | Chesterfield Town | ▲Elected to the League |
| 17 | Middlesbrough | ▲Elected to the League |
| 15 | Blackpool | ▼Not Re-Elected to the League |
| 11 | Stockport County | Not Elected to the League |
| 7 | Chorley | Not Elected to the League |
| 7 | Wigan County | Not Elected to the League |
| 0 | Coventry City | Not Elected to the League |
| 0 | Ashton North End | Not Elected to the League |
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End of Season Notes |
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▼Bolton Wanderers were Relegated from the Football League First Division |
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▼The Wednesday were Relegated from the Football League First Division |
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▲Manchester City were Promoted to the Football League First Division |
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▲Glossop North End were Promoted to the Football League First Division and changed their name to Glossop before the start of the 1899/00 Season |
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- Loughborough were Re-Elected to the Football League |
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▼Blackpool were Not Re-Elected to the Football League |
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▼Darwen did not seek Re-Election and Resigned from the Football League |
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▲Chesterfield Town were Elected to the Football League |
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▲Middlesbrough were Elected to the Football League |