| EFLT | 2022-2023 | 20/09/2022 | Tranmere Rovers | 2-2 | Bolton Wanderers | Keiran Sadlier, Conor Carty | Highlights | 1,779 | Draw |
| L2 | 2020-2021 | 23/01/2021 | Tranmere Rovers | 2-1 | Bolton Wanderers | Antoni Sarcevic | Highlights | Unknown | Loss |
| L2 | 2020-2021 | 19/12/2020 | Bolton Wanderers | 0-3 | Tranmere Rovers | | Highlights | Unknown | Loss |
| L1 | 2019-2020 | 01/02/2020 | Bolton Wanderers | 2-0 | Tranmere Rovers | Dennis Politic, Chris O'Grady | Highlights | 13,044 | Win |
| L1 | 2019-2020 | 17/08/2019 | Tranmere Rovers | 5-0 | Bolton Wanderers | | Highlights | 8,568 | Loss |
| LC2 | 2013-2014 | 27/08/2013 | Tranmere Rovers | 1-1 | Bolton Wanderers | Beckford (aet) (Lost 4-2 on penalties) | Highlights | 3,379 | Draw |
| LC2 | 2009-2010 | 25/08/2009 | Tranmere Rovers | 0-1 | Bolton Wanderers | Davies M | Highlights | 5,381 | Win |
| FAC3R | 2003-2004 | 13/01/2004 | Bolton Wanderers | 1-2 | Tranmere Rovers | Shakes (aet) | | 8,759 | Loss |
| FAC3 | 2003-2004 | 03/01/2004 | Tranmere Rovers | 1-1 | Bolton Wanderers | Nolan | | 10,587 | Draw |
| D1 | 2000-2001 | 13/01/2001 | Bolton Wanderers | 2-0 | Tranmere Rovers | Hansen, Hill (og) | | 15,493 | Win |
| D1 | 2000-2001 | 28/08/2000 | Tranmere Rovers | 0-1 | Bolton Wanderers | Whitlow | | 9,350 | Win |
| LCSFL2 | 1999-2000 | 26/01/2000 | Tranmere Rovers | 3-0 | Bolton Wanderers | | Highlights | 15,834 | Loss |
| LCSFL1 | 1999-2000 | 12/01/2000 | Bolton Wanderers | 0-1 | Tranmere Rovers | | Highlights | 13,303 | Loss |
| D1 | 1999-2000 | 04/12/1999 | Bolton Wanderers | 2-3 | Tranmere Rovers | Gudjohnsen, Taylor B | | 13,534 | Loss |
| D1 | 1999-2000 | 07/08/1999 | Tranmere Rovers | 0-0 | Bolton Wanderers | | | 7,674 | Draw |
| D1 | 1998-1999 | 12/12/1998 | Tranmere Rovers | 1-1 | Bolton Wanderers | Taylor B | | 6,959 | Draw |
| D1 | 1998-1999 | 14/11/1998 | Bolton Wanderers | 2-2 | Tranmere Rovers | Johansen, Holdsworth (pen) | | 16,564 | Draw |
| D1 | 1996-1997 | 04/05/1997 | Tranmere Rovers | 2-2 | Bolton Wanderers | McGinlay, Pollock | Highlights | 14,309 | Draw |
| D1 | 1996-1997 | 15/10/1996 | Bolton Wanderers | 1-0 | Tranmere Rovers | Sellars | | 14,136 | Win |
| D1 | 1994-1995 | 14/04/1995 | Tranmere Rovers | 1-0 | Bolton Wanderers | | | 15,595 | Loss |
| D1 | 1994-1995 | 27/12/1994 | Bolton Wanderers | 1-0 | Tranmere Rovers | Thompson A | | 16,782 | Win |
| D1 | 1993-1994 | 23/01/1994 | Bolton Wanderers | 2-1 | Tranmere Rovers | McGinlay (2) | Highlights | 11,550 | Win |
| D1 | 1993-1994 | 09/10/1993 | Tranmere Rovers | 2-1 | Bolton Wanderers | Brown P | | 10,128 | Loss |
| AITQ | 1993-1994 | 07/09/1993 | Tranmere Rovers | 1-2 | Bolton Wanderers | McGinlay, Coyle | | 2,786 | Win |
| D3PF | 1990-1991 | 01/06/1991 | Bolton Wanderers | 0-1 | Tranmere Rovers | (played at Wembley Stadium) | Highlights | 30,217 | Loss |
| D3 | 1990-1991 | 01/03/1991 | Tranmere Rovers | 1-1 | Bolton Wanderers | Patterson | | 10,076 | Draw |
| D3 | 1990-1991 | 01/12/1990 | Bolton Wanderers | 2-1 | Tranmere Rovers | Green, Philliskirk | | 6,941 | Win |
| AMCQ | 1990-1991 | 06/11/1990 | Bolton Wanderers | 1-0 | Tranmere Rovers | Reeves | | 3,178 | Win |
| D3 | 1989-1990 | 14/04/1990 | Bolton Wanderers | 1-1 | Tranmere Rovers | Storer | | 9,070 | Draw |
| AMCNSF | 1989-1990 | 20/02/1990 | Tranmere Rovers | 2-1 | Bolton Wanderers | Philliskirk | | 9,315 | Loss |
| D3 | 1989-1990 | 06/01/1990 | Tranmere Rovers | 1-3 | Bolton Wanderers | Cowdrill, Darby, Storer | | 8,273 | Win |
| D4 | 1987-1988 | 01/03/1988 | Bolton Wanderers | 2-0 | Tranmere Rovers | Thompson S, Thomas J | | 3,979 | Win |
| D4 | 1987-1988 | 15/12/1987 | Tranmere Rovers | 2-0 | Bolton Wanderers | | | 3,064 | Loss |
| FAC2 | 1986-1987 | 06/12/1986 | Bolton Wanderers | 2-0 | Tranmere Rovers | Caldwell, Thompson S | | 6,193 | Win |
| AMCNQF | 1985-1986 | 11/03/1986 | Bolton Wanderers | 2-1 | Tranmere Rovers | Caldwell, Oghani | | 3,865 | Win |
| FAC1R | 1983-1984 | 22/11/1983 | Bolton Wanderers | 4-1 | Tranmere Rovers | Chandler 2 (1 pen), Rudge, Caldwell (aet) | | 6,305 | Win |
| FAC1 | 1983-1984 | 19/11/1983 | Tranmere Rovers | 2-2 | Bolton Wanderers | Joyce W G, Chandler (pen) | | 5,497 | Draw |
| D3 | 1972-1973 | 26/12/1972 | Tranmere Rovers | 1-1 | Bolton Wanderers | Jones G | | 14,356 | Draw |
| D3 | 1972-1973 | 23/09/1972 | Bolton Wanderers | 2-0 | Tranmere Rovers | Jones G (pen), Wright R | | 6,139 | Win |
| D3 | 1971-1972 | 03/04/1972 | Bolton Wanderers | 1-0 | Tranmere Rovers | Byrom | | 6,216 | Win |
| D3 | 1971-1972 | 24/09/1971 | Tranmere Rovers | 0-0 | Bolton Wanderers | | | 6,988 | Draw |