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