In 1965, a new freight yard and goods shed were established to the west of the original one, followed by the September 1967 opening of a new station building (the present-day structure).

In its early years, the Napier Express passed through Masterton station before being re-routed along the west coast when the Wellington and Manawatu Railway Company's line was purchased in December 1908.

But because of insufficient patronage, through trains between Palmerston North and Masterton officially ceased on Monday, 1 August 1988, with the last services running on Friday, 29 July 1988.

Presently, the only passenger services with scheduled stops at this station are those of the Wairarapa Connection, which operates between Wellington and Masterton.

There are also a number of weekday freight services to/from Wellington, usually to the Juken Nissho timber mill just south at Waingawa with the locomotive regularly turned on the turntable.