Auckland's first railway, a 13-kilometre line to Onehunga, opened in 1873, built by the contracting firm Brogdens. The track crept south into the Waikato, reaching Mercer by 1875 and Te Awamutu by 1880. Then it stopped. An economic downturn froze construction for five years, and the King Country beyond Te Awamutu was not accessible to Europeans until 1883, when negotiations with local Maori opened the way. From the south, the Wellington and Manawatu Railway Company built its section between 1881 and 1886, connecting the capital to Palmerston North. The Longburn to Marton section had already been opened in 1878 as part of a line linking the ports of Foxton and Whanganui. The central section, the section everyone dreaded, began construction on 15 April 1885 when paramount chief Wahanui of Ngati Maniapoto turned the first sod outside Te Awamutu.

The central North Island presented the most formidable engineering challenges in New Zealand's railway history. The terrain rose too steeply for a direct route between the Whanganui River valleys and the North Island Volcanic Plateau. Four route options were surveyed before the Minister of Public Works chose the present corridor in 1884, and when surveyors realized just how difficult that route was, two more alternatives were studied in 1888. The solution that emerged included the famous Raurimu Spiral, where trains loop, tunnel, and hairpin their way up 132 metres over 6.8 kilometres, covering a straight-line distance of only two kilometres. The ruling gradient was set at 1 in 50, the steepest grade considered workable for heavy steam trains. Much of the initial construction was temporary, with unballasted track and vertical-sided cuttings through unstable country north of Taonui.

The idea of electrifying the NIMT surfaced as early as 1918, when electrical engineer Evan Parry argued that the network was straining under ever-increasing freight volumes and that cheap hydro-electricity in the central North Island could power a conversion from steam. The Wellington to Paekakariki section was electrified at 1500 volts DC in 1940, largely to prevent smoke problems in the 4.3-kilometre tunnel on the Tawa Flat deviation. In 1988, the 411-kilometre central section between Palmerston North and Hamilton was electrified at 25 kilovolts AC as part of the government's Think Big energy program. The economics were undermined when oil prices fell in the 1980s, and the final cost of 250 million dollars far exceeded the projected 100 million. But the capability was dramatic: where a diesel locomotive could haul 720-tonne trains at 27 kilometres per hour up the Raurimu Spiral, an electric locomotive could haul 1,100-tonne trains at 45 kilometres per hour.

The NIMT has been described as an engineering miracle, and the infrastructure bears that out: 352 bridges and 14 tunnels along its length, with five viaducts standing over 70 metres high. Between 1973 and 1981, the major Mangaweka deviation replaced aging tunnels in unstable terrain with three new viaducts crossing the Rangitikei and Kawhatau rivers. The curved metal viaduct at Hapuawhenua was replaced with a modern concrete structure during the 1980s electrification upgrades, though the original was preserved as a heritage attraction. In 1980, the 1880s Poro-O-Tarao Tunnel was replaced to allow clearance for large high-cube shipping containers. The line continues to evolve. In 2024, electrification was extended from Papakura to Pukekohe in the Auckland suburban network, leaving an 87-kilometre gap to the central electrified section at Te Rapa that may one day close, completing an electric spine the length of the North Island.