The 27-year-old's previous deal with the Shrimpers expired earlier this summer.
Deegan joined Phil Brown's side before the start of last season after being released by Northampton Town.
Southend start the new campaign with a trip to Fleetwood Town on Saturday.
Restore Data
| Team | P | W | D | L | F | A | GD | PTS | |
| 1 | Barnet | 22 | 15 | 2 | 5 | 46 | 25 | 21 | 47 |
| 2 | York City | 22 | 13 | 6 | 3 | 44 | 20 | 24 | 45 |
| 3 | Forest Green RoversForest Green | 21 | 13 | 6 | 2 | 39 | 17 | 22 | 45 |
| 4 | Gateshead | 22 | 12 | 5 | 5 | 41 | 27 | 14 | 41 |
| 5 | Oldham AthleticOldham | 20 | 11 | 7 | 2 | 36 | 19 | 17 | 40 |
| 6 | Rochdale | 21 | 11 | 3 | 7 | 31 | 19 | 12 | 36 |
| 7 | AltrinchamAltrincham | 22 | 9 | 7 | 6 | 36 | 28 | 8 | 34 |
| 8 | Yeovil TownYeovil | 22 | 10 | 4 | 8 | 27 | 23 | 4 | 34 |
| 9 | Halifax TownHalifax | 22 | 9 | 7 | 6 | 25 | 22 | 3 | 34 |
| 10 | Solihull MoorsSolihull | 22 | 9 | 5 | 8 | 38 | 35 | 3 | 32 |
| 11 | Sutton UnitedSutton | 22 | 9 | 5 | 8 | 29 | 27 | 2 | 32 |
| 12 | Hartlepool UnitedHartlepool | 22 | 7 | 9 | 6 | 24 | 24 | 0 | 30 |
| 13 | Eastleigh | 21 | 7 | 8 | 6 | 29 | 28 | 1 | 29 |
| 14 | Dagenham & RedbridgeDag & Red | 21 | 7 | 7 | 7 | 35 | 26 | 9 | 28 |
| 15 | Southend UnitedSouthend | 22 | 6 | 9 | 7 | 24 | 24 | 0 | 27 |
| 16 | Tamworth | 21 | 7 | 5 | 9 | 23 | 37 | -14 | 26 |
| 17 | Aldershot TownAldershot | 22 | 5 | 7 | 10 | 31 | 39 | -8 | 22 |
| 18 | Fylde | 22 | 6 | 4 | 12 | 27 | 43 | -16 | 22 |
| 19 | Woking | 22 | 5 | 6 | 11 | 19 | 32 | -13 | 21 |
| 20 | WealdstoneWealdstone | 21 | 4 | 8 | 9 | 24 | 32 | -8 | 20 |
| 21 | Braintree TownBraintree | 22 | 5 | 5 | 12 | 19 | 31 | -12 | 20 |
| 22 | Maidenhead UnitedMaidenhead | 22 | 5 | 5 | 12 | 27 | 44 | -17 | 20 |
| 23 | Boston UnitedBoston | 22 | 3 | 6 | 13 | 19 | 37 | -18 | 15 |
| 24 | Ebbsfleet | 22 | 1 | 6 | 15 | 16 | 50 | -34 | 9 |
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