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 | Port Vale | 14 | 9 | 3 | 2 | 23 | 15 | 8 | 30 |
| 2 | Walsall | 13 | 8 | 2 | 3 | 26 | 14 | 12 | 26 |
| 3 | Notts County | 14 | 7 | 5 | 2 | 22 | 12 | 10 | 26 |
| 4 | Doncaster RoversDoncaster | 14 | 8 | 2 | 4 | 20 | 16 | 4 | 26 |
| 5 | Crewe AlexandraCrewe | 13 | 7 | 3 | 3 | 16 | 12 | 4 | 24 |
| 6 | Chesterfield | 14 | 5 | 7 | 2 | 28 | 15 | 13 | 22 |
| 7 | Bradford CityBradford | 14 | 6 | 4 | 4 | 20 | 15 | 5 | 22 |
| 8 | MK Dons | 14 | 6 | 3 | 5 | 21 | 16 | 5 | 21 |
| 9 | BarrowBarrow | 14 | 6 | 3 | 5 | 15 | 11 | 4 | 21 |
| 10 | Grimsby Town | 14 | 7 | 0 | 7 | 18 | 25 | -7 | 21 |
| 11 | Gillingham | 14 | 6 | 2 | 6 | 15 | 12 | 3 | 20 |
| 12 | Salford City | 14 | 5 | 5 | 4 | 14 | 16 | -2 | 20 |
| 13 | AFC Wimbledon | 11 | 6 | 1 | 4 | 18 | 9 | 9 | 19 |
| 14 | Newport CountyNewport | 14 | 6 | 1 | 7 | 18 | 24 | -6 | 19 |
| 15 | Fleetwood TownFleetwood | 13 | 4 | 6 | 3 | 19 | 15 | 4 | 18 |
| 16 | Cheltenham TownCheltenham | 14 | 5 | 2 | 7 | 18 | 21 | -3 | 17 |
| 17 | Harrogate TownHarrogate | 14 | 4 | 3 | 7 | 11 | 19 | -8 | 15 |
| 18 | Bromley | 13 | 3 | 5 | 5 | 15 | 17 | -2 | 14 |
| 19 | Tranmere RoversTranmere | 13 | 3 | 5 | 5 | 8 | 16 | -8 | 14 |
| 20 | Accrington StanleyAccrington | 13 | 3 | 4 | 6 | 15 | 22 | -7 | 13 |
| 21 | Colchester UnitedColchester | 13 | 2 | 6 | 5 | 16 | 20 | -4 | 12 |
| 22 | Swindon TownSwindon | 14 | 2 | 6 | 6 | 15 | 20 | -5 | 12 |
| 23 | Carlisle UnitedCarlisle | 14 | 2 | 2 | 10 | 12 | 28 | -16 | 8 |
| 24 | Morecambe | 14 | 1 | 4 | 9 | 12 | 25 | -13 | 7 |
| > League Two Full Table | |||||||||
