The station was opened on 20 May 1875, although some services were available from October 1874. Goods services were closed on 3 November 1986. Prior to October 2012, the station had an island platform between the main lines, complete with original wooden station building and signal panel, and a suburban side platform to the west. It had a bowstring footbridge connecting the platforms, which dated from at least the 1930s, constructed of old railway iron and sleepers.
Upgrades
In 2007, the island platform was extended to the north, and new shelters were installed. Sidings were commissioned at the east of the station yard for stabling trains overnight. The heritage footbridge was demolished and scrapped, despite some local opposition, and replaced with a concrete bridge with two passenger lifts. The upgrade cost NZ$4,900,000 and was paid for as part of the Auckland Regional Transport Authority's system-wide upgrade of stations. Platforms were lengthened to enable six-car trains, because of anticipated growth in passenger numbers. 3,000 people passed through each day as of 2007, and another thousand were anticipated to use the station within five years. The new station was the seventh station to be redeveloped by ARTA in 2007. In 2012–2013, KiwiRail funded a significant upgrade as part of the Auckland Electrification Project, and to provide resiliency for suburban trains and freight trains heading south. The signalling was completely replaced; the signal panel had been commissioned over 80 years ago. The heritage station building was relocated to the western suburban platform, Platform 3, on 11 August 2012. The building was refurbished and restored, and contains the preserved signal panel on display, a ticket office, public toilets and space for a coffee kiosk. The North Island Main Trunk has been slewed to the east, with the island Platforms 1 and 2 adjacent to the Up main line to Auckland, typically serving suburban trains from Britomart to Pukekohe. The western suburban Platform 3 has been lengthened, and a new bay platform 4 at its southern extremity will serve DMU shuttles to Pukekohe. Bus stops are directly outside the ticket office, with the old bus stops on the station side of Railway Street West now only used for intercity services, and "rail buses" that operate when the railway network is shut down.
Services
Rail
The station is the terminus for suburban passenger trains on the Southern Line, which was electrified in 2015. An hourly diesel trainshuttle service runs between Papakura and Pukekohe on non-electrified track using DMUs. The station also serves the Auckland-Wellington Northern Explorer service, between stops at Strand and Hamilton. From 2020, the station will be the terminus of the revived Waikato Connection, to be named Te Huia. In May 2012, Auckland Transport's board included an investigation to extend electrified services to Pukekohe in its 10-year integrated transport plan. In April 2018 it was announced that electrification would be extended south to Pukekohe; see Auckland railway electrification.
Buses
Papakura is served by bus routes 33, 365, 371, 372, 373, 376, 377, 378 and 395.