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 | |
| C | Stockport CountyStockport | 45 | 27 | 11 | 7 | 95 | 46 | 49 | 92 |
| P | Mansfield TownMansfield | 45 | 24 | 13 | 8 | 89 | 46 | 43 | 85 |
| P | Wrexham | 45 | 25 | 10 | 10 | 87 | 51 | 36 | 85 |
| 4 | MK Dons | 45 | 23 | 8 | 14 | 79 | 64 | 15 | 77 |
| 5 | Doncaster RoversDoncaster | 45 | 21 | 7 | 17 | 71 | 66 | 5 | 70 |
| 6 | Crewe AlexandraCrewe | 45 | 19 | 13 | 13 | 68 | 64 | 4 | 70 |
| 7 | BarrowBarrow | 45 | 18 | 14 | 13 | 61 | 55 | 6 | 68 |
| 8 | Crawley TownCrawley | 45 | 20 | 7 | 18 | 71 | 67 | 4 | 67 |
| 9 | Bradford CityBradford | 45 | 18 | 12 | 15 | 57 | 58 | -1 | 66 |
| 10 | Walsall | 45 | 18 | 11 | 16 | 68 | 68 | 0 | 65 |
| 11 | Gillingham | 45 | 18 | 9 | 18 | 44 | 55 | -11 | 63 |
| 12 | AFC Wimbledon | 45 | 16 | 14 | 15 | 59 | 50 | 9 | 62 |
| 13 | Harrogate TownHarrogate | 45 | 17 | 11 | 17 | 58 | 67 | -9 | 62 |
| 14 | Notts County | 45 | 18 | 7 | 20 | 89 | 85 | 4 | 61 |
| 15 | Tranmere RoversTranmere | 45 | 17 | 6 | 22 | 66 | 66 | 0 | 57 |
| 16 | Morecambe | 45 | 17 | 9 | 19 | 64 | 78 | -14 | 57 |
| 17 | Newport CountyNewport | 45 | 16 | 7 | 22 | 61 | 72 | -11 | 55 |
| 18 | Accrington StanleyAccrington | 45 | 15 | 9 | 21 | 59 | 70 | -11 | 54 |
| 19 | Swindon TownSwindon | 45 | 14 | 11 | 20 | 74 | 80 | -6 | 53 |
| 20 | Salford City | 45 | 13 | 11 | 21 | 64 | 80 | -16 | 50 |
| 21 | Grimsby Town | 45 | 11 | 16 | 18 | 57 | 72 | -15 | 49 |
| 22 | Colchester UnitedColchester | 45 | 11 | 11 | 23 | 58 | 79 | -21 | 44 |
| 23 | Sutton UnitedSutton | 45 | 9 | 14 | 22 | 55 | 80 | -25 | 41 |
| R | Forest Green RoversForest Green | 45 | 10 | 9 | 26 | 43 | 78 | -35 | 39 |
| > League Two Full Table | |||||||||
