Robert FitzRoy was born at Ampton Hall, Ampton, Suffolk, England, into the upper echelons of the British aristocracy and a tradition of public service. Through his father,General Lord Charles FitzRoy, Robert was a fourth great-grandson of Charles II of England and his grandfather was Augustus Henry FitzRoy, 3rd Duke of Grafton. His mother was the daughter of the first Marquess of Londonderry and the half-sister of Viscount Castlereagh, who became Home Secretary. From the age of four Robert FitzRoy lived at Wakefield Lodge in Northamptonshire, the Palladian mansion of the FitzRoy family.

Robert's half-brother Sir Charles FitzRoy was Governor of New South Wales, Governor of Prince Edward Island and Governor of Antigua. FitzRoy was also the father of the Commander of the Channel, Rear-Admiral Sir Robert FitzRoy.

In February 1818, 12 years old, he entered the Royal Naval College, Portsmouth, and in the following year he entered the Royal Navy. At the age of 14 he embarked as a voluntary student aboard the frigate HMS Owen Glendower, which sailed to South America in the middle of 1820, and returned in January 1822. He was promoted to midshipman while on the vessel. FitzRoy then served on HMS Hind as a midshipman. He completed his course with distinction and was promoted lieutenant on 7 September 1824, having passed the examination with 'full numbers' (100%), a result not achieved previously. After serving on HMS Thetis, in 1828 he was appointed flag lieutenant to Rear-Admiral Sir Robert Waller Otway, commander-in-chief of the South American station, aboard HMS Ganges.

At that time HMS Beagle under Captain Pringle Stokes was carrying out a hydrographic survey of Tierra del Fuego, under the overall command of captain Phillip Parker King in HMS Adventure. Pringle Stokes became severely depressed and shot himself, and the ship under Lieutenant Skyring sailed to Rio de Janeiro, where Otway made FitzRoy (temporary) Captain of the Beagle on 15 December 1828. By the ship's return on 14 October 1830, FitzRoy had established his reputation as a surveyor and commander.

During the survey, some of his men were camping onshore when a group of Fuegian natives made off with their boat. His ship gave chase and, after a scuffle, the culprit's families were brought on board as hostages. Eventually FitzRoy held a boy, a girl and two men. As it was not possible to put them ashore conveniently he decided to 'civilise' the 'savages', teaching them "English ... the plainer truths of Christianity ... and the use of common tools" before returning them as missionaries. They were given names: the girl he called Fuegia Basket (so named because the replacement for the stolen boat was an improvised coracle that resembled a basket), the boy Jemmy Button (he was purchased by FitzRoy with buttons) and the one man who did not escape he named York Minster (named after the large rock near which he was captured). There was also a boy called Boat Memory. FitzRoy brought them back to England where Boat Memory died following a smallpox vaccination. The others were minded by the trainee missionary Richard Matthews and became 'civilised' enough to be presented at court in the summer of 1831.

In early May 1831 FitzRoy stood as Tory candidate for Ipswich in the General Election, but was defeated. His hopes of obtaining a new posting and organising a missionary project appeared to be failing, and he was organising the charter of a ship at his own expense to return the Fuegians with Matthews when his friend Francis Beaufort, Hydrographer to the British Admiralty, and his "kind uncle", the Duke of Grafton, interceded on his behalf at the Admiralty. On 25 June 1831 he was re-appointed commander of the Beagle. He spared no expense in fitting out the ship.

Very conscious of the stressful loneliness of command and of the suicide both of Captain Stokes and of his uncle Viscount Castlereagh, who had cut his own throat in 1822 while in government office, he approached Beaufort in August 1831 and asked him to find a suitable gentleman companion for the voyage. Such a companion should share his scientific tastes, make good use of the expedition's opportunities for naturalism research, dine with him as an equal, and provide a semblance of normal human friendship. While those Beaufort first approached turned the opportunity down, FitzRoy eventually approved Charles Darwin for the position. Before they left England FitzRoy gave Darwin a copy of the first volume of Charles Lyell's Principles of Geology, a book the captain had read that explained terrestrial features as the outcome of a gradual process taking place over extremely long periods. Moreover, FitzRoy took a request from Lyell himself to record observations on geological features such as erratic boulders.

FitzRoy and Darwin got on well together, but over the five-year survey voyage FitzRoy's violent temper — his outbursts had gained him the nickname "Hot Coffee" — occasioned quarrels sometimes "bordering on insanity", as Darwin later recalled. On a memorable occasion in March 1832 at Bahia, Brazil, Darwin was horrified at tales of the treatment of slaves, but FitzRoy, while not endorsing brutality, recounted how an estancia owner once asked his slaves if they wished to be free and was told they didn't. Darwin incautiously asked FitzRoy if he thought slaves could answer such a question honestly when it was posed by their master, at which the captain lost his temper and, before storming out, told Darwin that if he doubted his word they could no longer live together; effectively he banished Darwin from his table. Before nightfall FitzRoy's temper cooled and he sent a handsome apology with the request that Darwin "continue to live with him", so they avoided the subject of slavery from that time on. However, none of their quarrels were over religious or doctrinal issues — such disagreements came after the voyage.

At the island of "Buttons Land" in Tierra del Fuego they set up a mission post, but when they returned nine days later the possessions had been looted. Matthews gave up, rejoining the ship and leaving the three westernised Fuegians to continue the missionary work. While in the Falkland Islands, FitzRoy bought a schooner out of his own funds to assist with the surveying tasks he had been asked to complete, and had it refitted and renamed Adventure, hoping that the cost would be reimbursed by the Admiralty. They returned to the mission post but found only Jemmy Button who had returned to native ways and refused the offer to go with them back to England.

At Valparaiso in 1834, while Darwin was away from the ship exploring the Andes, the Admiralty reprimanded FitzRoy for buying the Adventure. He took the criticism badly, selling the schooner and announcing they would go back to recheck his survey, then resigning his command with doubts about his own sanity. The ship's officers persuaded him to withdraw his resignation and continue as planned once Darwin returned to the ship. FitzRoy continued his voyage, sailing on to the Galapagos, Tahiti, New Zealand, Australia and South Africa, then detouring to Bahia in Brazil so that he could carry out an additional check to ensure the accuracy of his longitude measurements before returning to England.

Soon after the Beagle's return on 2 October 1836, FitzRoy married a young woman to whom he had long been engaged. Darwin was amazed, as not once during the entire five years of the trip had FitzRoy spoken about being engaged.

FitzRoy was awarded a gold medal by the Royal Geographical Society in 1837. Extracts from his diary read to the society on 8 May 1837 included the observation (page 115) "Is it not extraordinary, that sea-worn, rolled, shingle-stones, and alluvial accumulations, compose the greater portion of these plains? How vast, and of what immense duration, must have been the actions of these waters which smoothed the shingle-stones now buried in the deserts of Patagonia!"

FitzRoy then wrote his account of the voyage, including editing the notes of the previous captain of the Beagle, which was completed and published in May 1839 as the Narrative of the surveying voyages of H.M.S. Adventure and Beagle in four volumes including Darwin's Journal and Remarks, 1832 — 1836 as the third volume. FitzRoy's account includes a section of Remarks with reference to the Deluge in which he admits that having read works "by geologists who contradict, by implication, if not in plain terms, the authenticity of the Scriptures" and "while led away by sceptical ideas" he had remarked to a friend that the vast plain of sedimentary material they were crossing "could never have been effected by a forty days' flood" indicating that in his "turn of mind and ignorance of scripture" he was willing to disbelieve the Biblical account. Concerned that such ideas might "reach the eyes of young sailors" he earnestly explains in great detail his renewed commitment to a literal reading of the Bible, with arguments that rock layers high in the mountains containing sea shells are actually proof of Noah's Flood and that the six days of creation could not have extended over aeons because the grass, herbs and trees would have died out during the long nights. FitzRoy was clearly dissociating himself from the new ideas of Charles Lyell which he had accepted during the voyage, and from Darwin's account which embraced these ideas, instead asserting a new commitment under the influence of his very religious wife to the doctrine of the established Church of England.

FitzRoy was elected the Tory Member of Parliament for Durham in 1841, and appointed Acting Conservator of the River Mersey in 1842.

The first Governor of New Zealand, Captain William Hobson, R.N., died in late 1842 and the Church Missionary Society, which had a strong New Zealand presence, suggested FitzRoy as his successor. He took up his new task in December 1843. It was probably an impossible job. His instructions were to maintain order and protect the Māori, while satisfying the land hunger of the settlers pouring into the country. He was given very few military resources, and Government revenue, mainly from customs duties, was woefully inadequate.

One of his first tasks was to enquire into the circumstances surrounding the Wairau Massacre. He found the actions of the Colonists to have been illegal and wisely declined to take any action against Te Rauparaha, wisely because he did not have the troops to meet him on anything like equal terms. However, this left the New Zealand Company and the settlers feeling betrayed and angry. One outcome was the appointment of a Government Superintendent for the area, establishing a ruling presence. He also insisted that the New Zealand Company pay the Māori a realistic price for the land they claimed to have purchased. These moves made him very unpopular.

Land sales were a continuing vexatious issue. The settlers were eager to buy land and some Māori were willing to sell, but under the provisions of the Treaty of Waitangi, land sales could only happen with the Government as an intermediary, and were thus extremely slow. FitzRoy changed the rules to allow settlers to purchase Māori land directly, subject to a duty of ten shillings per acre ($2.50 per hectare). However, land sales proved slower than expected. To meet the financial shortfall, FitzRoy raised the customs duties, then replaced them with property and income taxes. All these expedients failed, and before long the Colony was faced with bankruptcy and FitzRoy was forced to begin issuing promissory notes, paper money without backing.

Meanwhile, the Māori in the far North, around the Bay of Islands, who had been the first to sign the Treaty of Waitangi, were feeling increasingly sidelined and resentful of the changes that had taken place in New Zealand. To signal their resentment, Hone Heke cut down the flagpole at Kororareka. Rather than address the problems FitzRoy had the flagpole re-erected. Hone Heke cut it down again, four times altogether; by the fourth occasion the First New Zealand War, sometimes called the Flagstaff War or the Northern War, was well under way. It soon became apparent that FitzRoy did not have the resources to bring about a quick end to the war. Meanwhile, the spokesmen for the New Zealand Company were active back in Great Britain and FitzRoy's Governorship was presented to the House of Commons in a very poor light. As a result, he was shortly afterwards recalled and replaced by George Grey, then Governor of South Australia. Grey was also given the backing and support that FitzRoy had needed but was denied.

However, FitzRoy was not disgraced. He returned to Britain and in September 1848 was made superintendent of the Royal Naval Dockyards at Woolwich and then in March 1849 was given his final sea command, the screw frigate HMS Arrogant. In 1851 he retired from active service, partly due to ill health, and in that year was elected to the Royal Society with the support of 13 fellows including Charles Darwin.

As the protégé of Francis Beaufort, he was in 1854 appointed, on the recommendation of the President of the Royal Society, as chief of a new department to deal with the collection of weather data at sea, with the title of Meteorological Statist to the Board of Trade and a staff of three. This was the forerunner of the modern Meteorological Office. He arranged for captains of ships to provide information, with tested instruments being loaned for this purpose, and for computation of the data collected. He also was responsible for the design and distribution of a type of barometer which on his recommendation was fixed at every port to be consulted by crews before setting to sea: stone housings for such barometers are still visible at many fishing harbours. The invention of several different types of barometers was attributed to him, and these became popular and continued in production into the 20th century, characteristically engraved with Admiral FitzRoy's special remarks on interpretation, such as "When rising: In winter the rise of the barometer presages frost".

A terrible storm in 1859 that caused the loss of the Royal Charter inspired FitzRoy to develop charts to allow predictions to be made, which he called "forecasting the weather", thus coining the term weather forecast. Fifteen land stations were established to use the new telegraph to transmit to him daily reports of weather at set times. The first daily weather forecasts were published in The Times in 1860, and in the following year a system was introduced of hoisting storm warning cones at the principal ports when a gale was expected. The "Weather Book" which he published in 1863 was far in advance of the scientific opinion of the time. The storm also caused the Crown to distribute storm glasses, then known as "FitzRoy's storm barometers," to many small fishing communities around the British Isles.

Unfortunately, many fishing fleet owners objected to gale warnings, requiring that fleets not leave the ports and under this pressure, FitzRoy's system was abandoned for a short time after his death. The fishing fleet owners reckoned without the pressure of the normal fishermen, for whom FitzRoy had been a hero, responsible for saving many lives and the system was reinstated shortly thereafter.

When The Origin of Species was published FitzRoy was dismayed and apparently felt guilty for his part in the theory's development. He was in Oxford on 30 June 1860 to present a paper on storms and attended the meeting of the British Association for the Advancement of Science at which Samuel Wilberforce attacked Darwin's theory. During the debate FitzRoy, seen as "a grey haired Roman nosed elderly gentleman", stood in the centre of the audience and "lifting an immense Bible first with both and afterwards with one hand over his head, solemnly implored the audience to believe God rather than man". As he admitted that The Origin of Species had given him "acutest pain", the crowd shouted him down.

In 1863 FitzRoy was promoted to Vice-Admiral due to seniority, but in the coming years internal and external troubles at the Meteorological Office, financial concerns as well as failing health and his struggle with depression took their toll. On April 30, 1865, Vice-Admiral FitzRoy committed suicide, using a straight razor in an echo of his uncle's death. His wife writes that he got out of bed one morning, went to his washroom, and there committed suicide.

Robert FitzRoy is buried in the front church yard of All Saints Church in Upper Norwood, London. His memorial was restored by the Meteorological Office in 1981.

Robert FitzRoy was married twice. In 1836 he married Mary Henrietta O'Brien, they had four children. In 1854, after the death of his first wife, he married Maria Isabella Smyth in London. They had one daughter, Laura Elizabeth.

FitzRoy died having exhausted his entire fortune (£6,000, the equivalent of £400,000 today) on public expenditure. When this came to light, in order to prevent his wife and daughter living in destitution, his friend and colleague Bartholomew Sulivan began an Admiral FitzRoy Testimonial Fund which succeeded in getting the government to pay back £3,000 of this sum (Darwin contributed a further £100). Queen Victoria gave the special favour of allowing his widow and daughter the use of apartments at Hampton Court Palace, until her death.

The book Sailing directions for South America of FitzRoy led Chilean hydrographer Francisco Hudson to infer the possible existence of sailing route through internal waters from Chiloé Archipelago to Straits of Magellan, but Hudson was however the first to realize that the Isthmus of Ofqui made this impossible.

Mount Fitz Roy (Argentina–Chile, at the extreme south of the continent) was named after him by the Argentine scientist and explorer Francisco Moreno. It is 3,440 m (11,286 ft) high. The aboriginals had not named it, and used the word Chaltén (meaning smoking mountain) for other peaks as well. Fitzroy River, in northern Western Australia, was named after him by Lieutenant John Lort Stokes who, at the time, commanded HMS Beagle (previously commanded by FitzRoy). The impressive South American conifer Fitzroya cupressoides is named after him as well as the Delphinus fitzroyi, a species of dolphin discovered by Darwin during his voyage aboard the Beagle. Fitzroy, Falkland Islands is also named after him.

A memorial to FitzRoy is constructed atop the Bahia Wulaia dome middens on Isla Navarino in Tierra del Fuego, South America. It was presented in his bicentenary (2005) and commemorates his 23 January 1833 landing on Wulaia Cove. Another memorial presented also in FitzRoy's bicentenary commemorates his Cape Horn landing on 19 April 1830.

On 4 February 2002, when the shipping forecast sea area Finisterre was renamed to avoid confusion with the Spanish forecast area of the same name, the new name chosen by the UK's Meteorological Office was "FitzRoy", in honour of their founder.

In 2005, a novel entitled This Thing of Darkness by Harry Thompson was published. The novel's plot followed the lives of FitzRoy, Darwin and others connected with the Beagle expeditions, following them between the years of 1828 and 1865. It was a nominee on the long list for the 2005 Man Booker Prize (although Thompson died in November 2005).

FitzRoy has been commemorated by the Fitzroy Building at the University of Plymouth, used by the School of Earth, Ocean and Environmental Science.

Vice-Admiral Robert FitzRoy was commemorated on two stamps issued by the Royal Mail for the Falkland Islands and St Helena.

In 2010 New Zealand's National Institute of Water and Atmospheric Research (NIWA) named its new IBM supercomputer "FitzRoy" in honour of Robert FitzRoy.