| 2006-12-30 | ChestervMilton Keynes DonsLeague Two · England | 0–3 | League Two · England |
| 2006-12-26 | TorquayvMilton Keynes DonsLeague Two · England | 0–2 | League Two · England |
| 2006-12-23 | Milton Keynes DonsvRochdaleLeague Two · England | 2–1 | League Two · England |
| 2006-12-16 | Milton Keynes DonsvWycombeLeague Two · England | 3–1 | League Two · England |
| 2006-12-09 | AccringtonvMilton Keynes DonsLeague Two · England | 3–4 | League Two · England |
| 2006-12-05 | Milton Keynes DonsvStockportLeague Two · England | 2–0 | League Two · England |
| 2006-11-25 | DarlingtonvMilton Keynes DonsLeague Two · England | 1–0 | League Two · England |
| 2006-11-18 | Milton Keynes DonsvShrewsburyLeague Two · England | 2–0 | League Two · England |
| 2006-11-04 | GrimsbyvMilton Keynes DonsLeague Two · England | 1–3 | League Two · England |
| 2006-10-28 | WalsallvMilton Keynes DonsLeague Two · England | 0–0 | League Two · England |
| 2006-10-21 | Milton Keynes DonsvHerefordLeague Two · England | 1–3 | League Two · England |
| 2006-10-14 | WrexhamvMilton Keynes DonsLeague Two · England | 1–2 | League Two · England |
| 2006-10-06 | Milton Keynes DonsvPeterboroLeague Two · England | 0–2 | League Two · England |
| 2006-09-30 | BarnetvMilton Keynes DonsLeague Two · England | 3–3 | League Two · England |
| 2006-09-26 | Milton Keynes DonsvTorquayLeague Two · England | 3–2 | League Two · England |
| 2006-09-23 | Milton Keynes DonsvChesterLeague Two · England | 1–2 | League Two · England |
| 2006-09-16 | LincolnvMilton Keynes DonsLeague Two · England | 2–3 | League Two · England |
| 2006-09-12 | SwindonvMilton Keynes DonsLeague Two · England | 2–1 | League Two · England |
| 2006-09-09 | Milton Keynes DonsvHartlepoolLeague Two · England | 0–0 | League Two · England |
| 2006-09-02 | Milton Keynes DonsvNotts CountyLeague Two · England | 3–2 | League Two · England |
| 2006-08-26 | BostonvMilton Keynes DonsLeague Two · England | 0–1 | League Two · England |
| 2006-08-19 | Milton Keynes DonsvBristol RvsLeague Two · England | 2–0 | League Two · England |
| 2006-08-12 | MacclesfieldvMilton Keynes DonsLeague Two · England | 1–2 | League Two · England |
| 2006-08-08 | MansfieldvMilton Keynes DonsLeague Two · England | 2–1 | League Two · England |
| 2006-08-05 | Milton Keynes DonsvBuryLeague Two · England | 2–1 | League Two · England |
| 2006-05-06 | RotherhamvMilton Keynes DonsLeague One · England | 0–0 | League One · England |
| 2006-04-29 | Milton Keynes DonsvTranmereLeague One · England | 1–2 | League One · England |
| 2006-04-22 | ChesterfieldvMilton Keynes DonsLeague One · England | 1–2 | League One · England |
| 2006-04-17 | Milton Keynes DonsvHartlepoolLeague One · England | 2–1 | League One · England |
| 2006-04-15 | SwindonvMilton Keynes DonsLeague One · England | 0–1 | League One · England |
| 2006-04-08 | OldhamvMilton Keynes DonsLeague One · England | 1–2 | League One · England |
| 2006-04-04 | Port ValevMilton Keynes DonsLeague One · England | 3–1 | League One · England |
| 2006-04-01 | Milton Keynes DonsvGillinghamLeague One · England | 1–2 | League One · England |
| 2006-03-28 | Milton Keynes DonsvBrentfordLeague One · England | 0–1 | League One · England |
| 2006-03-25 | Nott'm ForestvMilton Keynes DonsLeague One · England | 3–0 | League One · England |
| 2006-03-18 | Milton Keynes DonsvSouthendLeague One · England | 2–1 | League One · England |
| 2006-03-10 | Milton Keynes DonsvBristol CityLeague One · England | 0–1 | League One · England |
| 2006-02-25 | Milton Keynes DonsvBradfordLeague One · England | 2–1 | League One · England |
| 2006-02-18 | HuddersfieldvMilton Keynes DonsLeague One · England | 5–0 | League One · England |
| 2006-02-14 | YeovilvMilton Keynes DonsLeague One · England | 1–1 | League One · England |
| 2006-02-11 | Milton Keynes DonsvBlackpoolLeague One · England | 3–0 | League One · England |
| 2006-02-04 | ScunthorpevMilton Keynes DonsLeague One · England | 2–0 | League One · England |
| 2006-01-31 | Milton Keynes DonsvNott'm ForestLeague One · England | 1–0 | League One · England |
| 2006-01-21 | BarnsleyvMilton Keynes DonsLeague One · England | 2–0 | League One · England |
| 2006-01-14 | Milton Keynes DonsvYeovilLeague One · England | 1–1 | League One · England |
| 2006-01-10 | SwanseavMilton Keynes DonsLeague One · England | 3–1 | League One · England |
| 2006-01-02 | Milton Keynes DonsvOldhamLeague One · England | 0–1 | League One · England |