Key: Win : Draw : Loss
| Date | Home | Away | Ref | ||
|---|---|---|---|---|---|
| 04/08/2018 | Notts County | 0 | 0 | Colchester | S Stockbridge |
| 11/08/2018 | Colchester | 2 | 0 | Port Vale | M Donohue |
| 18/08/2018 | Mansfield | 1 | 1 | Colchester | M Salisbury |
| 21/08/2018 | Colchester | 6 | 0 | Crewe | N Hair |
| 25/08/2018 | Colchester | 1 | 2 | Northampton | A Young |
| 01/09/2018 | Cheltenham | 1 | 3 | Colchester | O Yates |
| 08/09/2018 | Tranmere | 1 | 1 | Colchester | R Lewis |
| 15/09/2018 | Colchester | 3 | 0 | Cambridge | L Swabey |
| 22/09/2018 | Oldham | 3 | 3 | Colchester | A Backhouse |
| 29/09/2018 | Colchester | 1 | 2 | Bury | T Bramall |
| 02/10/2018 | Colchester | 3 | 1 | Yeovil | C Hicks |
| 06/10/2018 | Stevenage | 3 | 1 | Colchester | N Kinseley |
| 13/10/2018 | Colchester | 3 | 1 | Crawley Town | T Kettle |
| 20/10/2018 | Morecambe | 0 | 1 | Colchester | A Haines |
| 23/10/2018 | Grimsby | 1 | 0 | Colchester | G Salisbury |
| 27/10/2018 | Colchester | 1 | 0 | Lincoln | D Coote |
| 03/11/2018 | Colchester | 1 | 0 | Swindon | D Whitestone |
| 17/11/2018 | Newport County | 2 | 0 | Colchester | R East |
| 24/11/2018 | Colchester | 1 | 1 | Exeter | B Toner |
| 27/11/2018 | Forest Green | 0 | 1 | Colchester | K Johnson |
| 08/12/2018 | Colchester | 1 | 0 | Macclesfield | N Hair |
| 15/12/2018 | Carlisle | 4 | 0 | Colchester | E Ilderton |
| 22/12/2018 | Milton Keynes Dons | 0 | 1 | Colchester | C Sarginson |
| 26/12/2018 | Colchester | 1 | 2 | Stevenage | L Collins |
| 29/12/2018 | Colchester | 0 | 0 | Morecambe | J Busby |
| 01/01/2019 | Crawley Town | 2 | 0 | Colchester | A Davies |
| 05/01/2019 | Colchester | 3 | 3 | Notts County | C Breakspear |
| 12/01/2019 | Port Vale | 0 | 3 | Colchester | S Oldham |
| 19/01/2019 | Colchester | 2 | 3 | Mansfield | B Huxtable |
| 26/01/2019 | Crewe | 2 | 1 | Colchester | P Wright |
| 02/02/2019 | Northampton | 0 | 4 | Colchester | R Joyce |
| 09/02/2019 | Colchester | 3 | 0 | Cheltenham | C Hicks |
| 16/02/2019 | Macclesfield | 1 | 1 | Colchester | A Haines |
| 23/02/2019 | Colchester | 1 | 1 | Carlisle | T Kettle |
| 02/03/2019 | Swindon | 3 | 0 | Colchester | O Yates |
| 09/03/2019 | Colchester | 3 | 0 | Newport County | L Collins |
| 12/03/2019 | Colchester | 0 | 3 | Forest Green | A Young |
| 16/03/2019 | Exeter | 3 | 0 | Colchester | S Oldham |
| 23/03/2019 | Colchester | 0 | 2 | Tranmere | R Joyce |
| 30/03/2019 | Cambridge | 0 | 1 | Colchester | D Drysdale |
| 06/04/2019 | Colchester | 0 | 2 | Oldham | L Swabey |
| 13/04/2019 | Bury | 2 | 0 | Colchester | A Haines |
| 19/04/2019 | Colchester | 1 | 0 | Grimsby | C Sarginson |
| 22/04/2019 | Yeovil | 1 | 1 | Colchester | P Wright |
| 27/04/2019 | Colchester | 2 | 0 | Milton Keynes Dons | A Coggins |
| 04/05/2019 | Lincoln | 0 | 3 | Colchester | T Kettle |