| L1 | 30/04/2017 | Bolton Wanderers | 3-0 | Peterborough United | Jem Karacan, David Wheater, Adam Le Fondre | Highlights | 22,590 | Win |
| L1 | 22/04/2017 | Port Vale | 0-2 | Bolton Wanderers | David Wheater, Gary Madine | Highlights | 8,890 | Win |
| L1 | 18/04/2017 | Bolton Wanderers | 0-0 | Bury | | Highlights | 18,223 | Draw |
| L1 | 15/04/2017 | Oldham Athletic | 1-0 | Bolton Wanderers | | Highlights | 8,788 | Loss |
| L1 | 08/04/2017 | Scunthorpe United | 1-0 | Bolton Wanderers | | Highlights | 6,149 | Loss |
| L1 | 04/04/2017 | Southend United | 0-1 | Bolton Wanderers | Mark Beevers | Highlights | 9,340 | Win |
| L1 | 01/04/2017 | Bolton Wanderers | 0-0 | Chesterfield | | Highlights | 23,376 | Draw |
| L1 | 25/03/2017 | Shrewsbury Town | 0-2 | Bolton Wanderers | Mark Beevers, Adam Le Fondre | Highlights | 7,532 | Win |
| L1 | 21/03/2017 | Oxford United | 2-4 | Bolton Wanderers | Filipe Morais, Mark Beevers, Own Goal, Josh Vela | Highlights | 7,146 | Win |
| L1 | 18/03/2017 | Bolton Wanderers | 2-1 | Northampton Town | Adam Le Fondre, Filipe Morais | Highlights | 14,255 | Win |
| L1 | 14/03/2017 | Gillingham | 0-4 | Bolton Wanderers | David Wheater, Adam Le Fondre, Mark Beevers, Josh Vela | Highlights | 5,199 | Win |
| L1 | 11/03/2017 | Fleetwood Town | 2-4 | Bolton Wanderers | Adam Le Fondre (2), David Wheater, Mark Beevers | Highlights | 5,123 | Win |
| L1 | 04/03/2017 | Bolton Wanderers | 1-1 | AFC Wimbledon | Gary Madine | Highlights | 13,599 | Draw |
| L1 | 28/02/2017 | Bolton Wanderers | 1-1 | Bristol Rovers | Josh Vela | Highlights | 13,383 | Draw |
| L1 | 25/02/2017 | Sheffield United | 2-0 | Bolton Wanderers | | Highlights | 27,165 | Loss |
| L1 | 18/02/2017 | Bradford City | 2-2 | Bolton Wanderers | David Wheater, Gary Madine | Highlights | 21,190 | Draw |
| L1 | 14/02/2017 | Bolton Wanderers | 1-0 | Rochdale | Mark Beevers | Highlights | 13,313 | Win |
| L1 | 11/02/2017 | Bolton Wanderers | 4-1 | Walsall | Gary Madine, Own Goal, Liam Trotter, Chris Long | Highlights | 13,610 | Win |
| L1 | 04/02/2017 | Milton Keynes Dons | 1-1 | Bolton Wanderers | Jay Spearing | Highlights | 21,545 | Draw |
| L1 | 28/01/2017 | Bolton Wanderers | 1-2 | Charlton Athletic | Zach Clough | Highlights | 13,265 | Loss |
| FAC3R | 17/01/2017 | Crystal Palace | 2-1 | Bolton Wanderers | James Henry | Highlights | 7,149 | Loss |
| L1 | 14/01/2017 | Bolton Wanderers | 1-2 | Swindon Town | David Wheater | Highlights | 13,955 | Loss |
| FAC3 | 07/01/2017 | Bolton Wanderers | 0-0 | Crystal Palace | | Highlights | 11,683 | Draw |
| L1 | 02/01/2017 | Coventry City | 2-2 | Bolton Wanderers | Zach Clough, Max Clayton | Highlights | 8,397 | Draw |
| L1 | 31/12/2016 | Bolton Wanderers | 2-1 | Scunthorpe United | Josh Vela, James Henry | Highlights | 17,062 | Win |
| L1 | 26/12/2016 | Bolton Wanderers | 2-1 | Shrewsbury Town | David Wheater (2) | Highlights | 16,238 | Win |
| L1 | 17/12/2016 | Chesterfield | 1-0 | Bolton Wanderers | | Highlights | 6,924 | Loss |
| L1 | 12/12/2016 | Bolton Wanderers | 4-0 | Gillingham | Gary Madine (2), Josh Vela, Sammy Ameobi | Highlights | 13,861 | Win |
| FAC2 | 04/12/2016 | Bolton Wanderers | 3-2 | Sheffield United | Gary Madine, Sammy Ameobi, Josh Vela | Highlights | 7,027 | Win |
| L1 | 26/11/2016 | Northampton Town | 0-1 | Bolton Wanderers | Zach Clough | Highlights | 7,018 | Win |
| L1 | 22/11/2016 | Bolton Wanderers | 1-0 | Coventry City | Zach Clough | Highlights | 12,290 | Win |
| L1 | 19/11/2016 | Bolton Wanderers | 2-0 | Millwall | Josh Vela, Tom Thorpe | Highlights | 13,110 | Win |
| L1 | 13/11/2016 | Peterborough United | 1-0 | Bolton Wanderers | | Highlights | 4,780 | Loss |
| EFLT | 08/11/2016 | Cheltenham Town | 1-0 | Bolton Wanderers | | Highlights | 1,038 | Loss |
| FAC1 | 05/11/2016 | Bolton Wanderers | 1-0 | Grimsby Town | Liam Trotter | Highlights | 6,649 | Win |
| L1 | 29/10/2016 | Bolton Wanderers | 3-1 | Port Vale | Zach Clough, Josh Vela, Andy Taylor | Highlights | 13,937 | Win |
| L1 | 24/10/2016 | Bury | 0-2 | Bolton Wanderers | Zach Clough (2) | Highlights | 8,007 | Win |
| L1 | 18/10/2016 | Millwall | 0-2 | Bolton Wanderers | Sammy Ameobi, David Wheater | Highlights | 7,898 | Win |
| L1 | 15/10/2016 | Bolton Wanderers | 2-0 | Oldham Athletic | Zach Clough (2) | Highlights | 14,891 | Win |
| L1 | 08/10/2016 | Swindon Town | 0-1 | Bolton Wanderers | Own Goal | Highlights | 7,023 | Win |
| EFLT | 04/10/2016 | Bolton Wanderers | 1-0 | Blackpool | Sammy Ameobi | Highlights | 1,589 | Win |
| L1 | 01/10/2016 | Bolton Wanderers | 0-2 | Oxford United | | Highlights | 14,207 | Loss |
| L1 | 27/09/2016 | Rochdale | 1-0 | Bolton Wanderers | | Highlights | 6,011 | Loss |
| L1 | 24/09/2016 | Bolton Wanderers | 0-0 | Bradford City | | Highlights | 17,486 | Draw |
| L1 | 17/09/2016 | Walsall | 1-0 | Bolton Wanderers | | Highlights | 5,962 | Loss |
| L1 | 10/09/2016 | Bolton Wanderers | 1-1 | Milton Keynes Dons | Mark Beevers | Highlights | 12,727 | Draw |
| L1 | 03/09/2016 | Bolton Wanderers | 1-1 | Southend United | Keshi Anderson | Highlights | 13,519 | Draw |
| EFLT | 30/08/2016 | Bolton Wanderers | 0-2 | Everton | | Highlights | 1,540 | Loss |
| L1 | 27/08/2016 | Charlton Athletic | 1-1 | Bolton Wanderers | Gary Madine | Highlights | 10,926 | Draw |
| L1 | 20/08/2016 | Bolton Wanderers | 2-1 | Fleetwood Town | Gary Madine, Josh Vela | Highlights | 13,524 | Win |
| L1 | 17/08/2016 | Bristol Rovers | 1-2 | Bolton Wanderers | Josh Vela, Jay Spearing | Highlights | 9,169 | Win |
| L1 | 13/08/2016 | AFC Wimbledon | 1-2 | Bolton Wanderers | Gary Madine, Liam Trotter | Highlights | 4,619 | Win |
| LC1 | 09/08/2016 | Blackpool | 4-2 | Bolton Wanderers | Jamie Proctor, Kaiyne Woolery | Highlights | 3,633 | Loss |
| L1 | 06/08/2016 | Bolton Wanderers | 1-0 | Sheffield United | Jay Spearing | Highlights | 17,050 | Win |