The England defender left Leeds in July 2002 for an initial £15m, while a further payment of £14.3m was paid a year later.
However Man Utd still owed further instalments on the deal - dependent on results - which could have seen it rise to £32.5m.
A Leeds United statement to the stock exchange read: "Leeds United Plc is pleased to announce the expected receipt tomorrow from Manchester United, via the FAPL, of £1.5m in full and final settlement of the contingent deferred sums due on the Rio Ferdinand transfer totaling £3.25m."
Leeds will receive the money on Thursday regardless of how successful Manchester United are this season, with Ferdinand currently serving a eight month ban due to missing a drugs test.
This now means that Leeds are a step closer to avoiding administration.