Network Rail said the junction was used by up to 500 trains a day, and the project – which cost £26m – took nearly a year of planning.
Workers replaced 130 track panels and renewed the foundation stone beneath the tracks.
There were also improvements made to points, switches and crossings.
Follow-up work is scheduled for Hanslope Junction on 11 and 25 January, with trains between Milton Keynes and Northampton suspended while it takes place.
While the line was closed, other projects took place nearby.
Uneven surfaces on platform 4 at Milton Keynes Central Station were replaced. Elsewhere in Buckinghamshire, there was resurfacing work on platforms 3 and 4 at Wolverton Station to improve stepping distances between trains and the platforms.
At Roade, Northamptonshire, about 1,500m of new rail was installed.