| 03 May 1999 | First Round | Broughton v Grimsby Town | Recreation Ground, Broughton | Results |
| 03 May 1999 | First Round | Millennium Chemicals v Louth | Clee Road, Grimsby | Results |
| 03 May 1999 | First Round | Market Rasen v Normanby Park Works | Rase Park, Market Rasen | Results |
| 03 May 1999 | First Round | Messingham v Keelby | Memorial Playing Field, Messingham | Results |
| 03 May 1999 | First Round | Rustons v Outcasts | Newark Road, Lincoln | Results |
| 03 May 1999 | First Round | Skegness v Bottesford Town | Richmond Drive, Skegness | Results |
| 03 May 1999 | First Round | Alford v Littlefields | Train Fen Holt, Alford | Results |
| 03 May 1999 | First Round | Hartsholme v Nettleton Mines | Ashby Avenue, Hartsholme | Results |
| 03 May 1999 | First Round | Barton Town Second XI v Holton-le-Clay | Marsh Lane, Barton on Humber | Results |
| 03 May 1999 | First Round | Bracebridge Heath Second XI v Haxey | Cross O'Cliff Court, Bracebridge Heath | Results |
| 03 May 1999 | First Round | Alkborough v Immingham Blossom Way | West Halton Lane, Alkborough | Results |
| 03 May 1999 | First Round | Cherry Willingham v Cleethorpes Third XI | Playing Fields, Cherry Willingham | Results |
| 03 May 1999 | First Round | Hykeham v Scunthorpe Town | Memorial Field, North Hykeham | Results |
| 03 May 1999 | First Round | Brigg Town v Caistor Town | Brigg Recreation Ground, Brigg | Results |
| 03 May 1999 | First Round | Nettleham v South Kelsey | Mulsanne Park, Nettleham | Results |
| 03 May 1999 | First Round | Owmby v Horncastle | Todmoor, Owmby by Spital | Results |
| 31 May 1999 | Second Round | Louth v Normanby Park Works | London Road, Louth | Results |
| 31 May 1999 | Second Round | Messingham v Outcasts | Memorial Playing Field, Messingham | Results |
| 31 May 1999 | Second Round | Skegness v Alford | Richmond Drive, Skegness | Results |
| 31 May 1999 | Second Round | Hartsholme v Holton-le-Clay | Ashby Avenue, Hartsholme | Results |
| 31 May 1999 | Second Round | Bracebridge Heath Second XI v Alkborough | Cross O'Cliff Court, Bracebridge Heath | Results |
| 31 May 1999 | Second Round | Hykeham v Cleethorpes Third XI | Memorial Field, North Hykeham | Results |
| 31 May 1999 | Second Round | Caistor Town v Nettleham | Brigg Road Ground, Caistor | Results |
| 31 May 1999 | Second Round | Owmby v Grimsby Town | Todmoor, Owmby by Spital | Results |
| 13 Jun 1999 | Quarter-Final | Louth v Messingham | London Road, Louth | Results |
| 13 Jun 1999 | Quarter-Final | Skegness v Hartsholme | Richmond Drive, Skegness | Results |
| 31 Aug 1999 | Quarter-Final | Alkborough v Cleethorpes Third XI | West Halton Lane, Alkborough | Results |
| 13 Jun 1999 | Quarter-Final | Caistor Town v Owmby | Brigg Road Ground, Caistor | Results |
| 11 Jul 1999 | Semi-Final | Messingham v Caistor Town | Memorial Playing Field, Messingham | Results |
| 11 Jul 1999 | Semi-Final | Skegness v Alkborough | Richmond Drive, Skegness | Results |
| 15 Aug 1999 | Final | Alkborough v Messingham | Augusta Street, Grimsby | Results |
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