The motives behind Cook's voyages, on the first of which he rediscovered New Zealand, were almost wholly scientific. His initial task was to observe the transit of Venus across the sun, at Tahiti. That done, he was to take the Endeavour south in search of the southern continent, or else to explore the eastern side of the land discovered by Tasman. On 6 October 1769 a boy sighted land, a cape named Young Nick's Head in his honour by Cook. The ship was anchored in a bay – Poverty Bay – and Cook, with Joseph Banks and Daniel Solander, two notable botanists who were making the voyage with him, went ashore. They could talk with the Maoris, thanks to the presence of a Tahitian, Tupaia, but this did not prevent bloodshed. The deaths which resulted from this initial affray were perhaps necessary, unless European lives were to be lost, but Cook was distressed. Some prisoners, taken in the affray, were well treated and put ashore. Canoes came out to the ship as it moved south around Table Cape, the great bay he called Hawke's Bay, and to Cape Kidnappers, so named to commemorate an attempt of some Maoris to snatch a Tahitian boy from the ship. Looking for a harbour and noting evidence of a considerable population, Cook went as far south as Cape Turnagain, and then sailed north. Five days were spent at Tolaga Bay, filling water casks, collecting vegetables, botanising, and observing the Maoris, with whom friendly relations this time persisted. After this respite the Endeavour rounded East Cape, scared off some hostile canoes at Hicks Bay, and entered the Bay of Plenty. The initial phase of discovery came to an end with the 11 days spent at Mercury Bay on the east coast of the Coromandel Peninsula. Here Cook took on water, wood, and vegetables, observed the transit of Mercury to fix his position exactly, and closely examined Maori life.

On 15 November Cook sailed north again, after a wholly friendly and profitable interlude, and having taken possession of the country in the name of the king. He rounded Cape Colville and sailed into the gulf which, together with its river, he called the Thames, turned north with the coast, and was prevented by bad weather from noting the existence of off-shore islands and of Waitemata harbour. He named Cape Brett, went as far north as the Cavalli Islands, and south again to the Bay of Islands, where he paused for some days, going ashore where, after an initial skirmish, he established good relations with the numerous and warlike natives. On 6 December the Endeavour put out to sea again.

A week later she was for the first time out of sight of land. Though held up by adverse weather, Cook managed to fix exactly the positions of North Cape, Three Kings and (on New Year's Day, 1770) Cape Maria van Diemen. He sailed, out of sight of land, as far as the entrance to Kaipara Harbour, and turned north along a barren coast. Cook then returned past Kawhia Harbour, and around the cape and mountain both of which he called Egmont. He followed the line of the coast until he came up against the high and broken coast of the South Island. He had in fact entered Cook Strait, and almost completed his circumnavigation of the North Island, though this was not yet known. On 14 January he put into a cove, since known as Ship Cove in Queen Charlotte Sound, for wood, water, and repairs.

While in this haven, which was to be Cook's base on future voyages, the ship was set to rights, the crew refreshed, and botanical specimens collected by Banks and Solander. The natives proved friendly, after some initial trouble, and one of them described to Cook the shape and size of New Zealand as he knew it. Cook explored by boat and on foot; from one peak he saw the ocean stretching away to the east and the strait separating the North from the South Island. He named Queen Charlotte Sound, and took possession of adjacent lands in the name of the king. The Endeavour left the sound on 6 February.

Cook cleared the strait, and to make it abundantly clear that the North Island was an island, sailed north to Cape Turnagain. He then turned south, observing the Seaward Kaikoura Range running parallel with the coast, went past Kaikoura Peninsula and on to Banks Peninsula, taken, because of the low-lying land separating its peaks from the mainland, for an island. A diversion to the south-east (an officer thought he saw land in this direction) took him out of sight of the coast which he regained on February 19. Cape Saunders (Otago Peninsula) was named, and the south-east coast of Otago regained after the ship was taken out to sea by bad weather. After some hesitation the island, later called Stewart Island, was charted as a peninsula. The southern coast was rounded, West Cape named, and the voyage up the west coast of the South Island commenced. Dusky Bay and Doubtful Harbour were named and passed, and the later part of March saw the Endeavour off the coast charted in the seventeenth century by Tasman. She passed Cape Foulwind and Cape Farewell, and sailed into Cook Strait to the entrance of Queen Charlotte Sound, thus completing the circumnavigation of the South Island. On 27 March Cook anchored in Admiralty Bay, to take on water and wood, and prepare for the long voyage home. Five days later Cook left New Zealand.

As a result of this voyage, New Zealand, in a real sense of the word, became known. Cook's chart was unusually complete and accurate; future discoverers could do no more than tidy up his outline. Something about the interior was known; that the North Island was the more fertile and the South more mountainous. Thanks to Banks and Solander, the flora and fauna had been scientifically observed. Thanks to Cook and Banks, some useful observations on the nature and habits of the Maoris had been set down. Two resources of the country, timber and flax, were described. Whether Cook's successors proved to be traders, missionaries, scientists, or settlers, they had something upon which to build.

He was to revisit New Zealand and use it as a base during his second and third voyages, voyages concerned with the exploration of the whole Pacific Ocean. In April 1773, on the Resolution, he entered Dusky Sound to refit the ship and recruit the crew. The Sound was meticulously charted. In May he left for Ship Cove, there to meet Tobias Furneaux and the Adventure; in June the two ships sailed east to find no continent, but to discover islands in the Pacific. Both ships, off Cook Strait again in October, parted company in a storm, and the Resolution, after pausing outside Port Nicholson, retired to Queen Charlotte Sound. In November Cook left for the Antarctic Ocean. Furneaux, who had been blown well north, reached the Sound soon after Cook departed and lost 10 of his men in an affray with the natives. Cook himself returned in October 1774, after a voyage which left no possible resting place for the southern continent, to discover the Tory Channel outlet to the Sound. His third visit, during his voyage in February 1777, was his last. Two years later he was killed at Hawaii.