The 23-year-old is a graduate of the Dons academy and made 13 appearances during their successful promotion from League One.
"I'm more excited to be staying than ever after the promotion," he told the club's official website. "I've been working hard in the off-season and I want to come back flying."
Flanagan made his first-team debut for MK Dons back in 2010.
Restore Data
| Team | P | W | D | L | F | A | GD | PTS | |
| 1 | Walsall | 29 | 18 | 5 | 6 | 55 | 32 | 23 | 59 |
| 2 | Notts County | 29 | 15 | 8 | 6 | 47 | 28 | 19 | 53 |
| 3 | Doncaster RoversDoncaster | 30 | 15 | 7 | 8 | 44 | 37 | 7 | 52 |
| 4 | Bradford CityBradford | 29 | 14 | 8 | 7 | 39 | 28 | 11 | 50 |
| 5 | AFC Wimbledon | 28 | 14 | 7 | 7 | 39 | 20 | 19 | 49 |
| 6 | Port Vale | 29 | 13 | 10 | 6 | 38 | 32 | 6 | 49 |
| 7 | Salford City | 30 | 13 | 9 | 8 | 38 | 29 | 9 | 48 |
| 8 | Crewe AlexandraCrewe | 30 | 12 | 12 | 6 | 36 | 28 | 8 | 48 |
| 9 | Grimsby Town | 30 | 14 | 3 | 13 | 42 | 46 | -4 | 45 |
| 10 | Chesterfield | 29 | 11 | 9 | 9 | 48 | 34 | 14 | 42 |
| 11 | Colchester UnitedColchester | 29 | 9 | 13 | 7 | 35 | 30 | 5 | 40 |
| 12 | Fleetwood TownFleetwood | 28 | 10 | 9 | 9 | 39 | 35 | 4 | 39 |
| 13 | Bromley | 30 | 9 | 12 | 9 | 40 | 40 | 0 | 39 |
| 14 | MK Dons | 29 | 11 | 5 | 13 | 42 | 41 | 1 | 38 |
| 15 | Swindon TownSwindon | 31 | 9 | 11 | 11 | 46 | 47 | -1 | 38 |
| 16 | Cheltenham TownCheltenham | 29 | 10 | 8 | 11 | 37 | 41 | -4 | 38 |
| 17 | Newport CountyNewport | 29 | 10 | 6 | 13 | 40 | 47 | -7 | 36 |
| 18 | BarrowBarrow | 29 | 9 | 7 | 13 | 30 | 32 | -2 | 34 |
| 19 | Gillingham | 28 | 9 | 5 | 14 | 25 | 32 | -7 | 32 |
| 20 | Accrington StanleyAccrington | 28 | 7 | 9 | 12 | 34 | 45 | -11 | 30 |
| 21 | Harrogate TownHarrogate | 31 | 8 | 6 | 17 | 25 | 42 | -17 | 30 |
| 22 | Tranmere RoversTranmere | 29 | 6 | 8 | 15 | 21 | 48 | -27 | 26 |
| 23 | Morecambe | 30 | 6 | 5 | 19 | 27 | 48 | -21 | 23 |
| 24 | Carlisle UnitedCarlisle | 29 | 5 | 6 | 18 | 23 | 48 | -25 | 21 |
| > League Two Full Table | |||||||||
