"I have settled several little commissions at Zanzibar satisfactorily. One was to get the Sultan to sign the concessions which Mackinnon tried to obtain a long time ago. As the Germans have magnificent territory east of Zanzibar, it was but fair that England should have some portion for the protection she has accorded to Zanzibar since 1841 .... The concession that we wished to obtain embraced a portion of East African coast, of which Mombasa and Melindi were the principal towns. For eight years, to my knowledge, the matter had been placed before His Highness, but the Sultan's signature was difficult to obtain."

Rowlands immigrated to the United States in 1859 at age 18. He disembarked at New Orleans and, according to his own declarations, became friends by accident with Henry Hope Stanley, a wealthy trader. He saw Stanley sitting on a chair outside his store and asked him if he had any job openings. He did so in the British style: "Do you need a boy, sir?" The childless man had indeed been wishing he had a son, and the inquiry led to a job and a close relationship between them. Out of admiration, John took Stanley's name. Later, he wrote that his adoptive parent died two years after their meeting, but in fact the elder Stanley did not die until 1878. This and other discrepancies led John Bierman to argue that no adoption took place. Tim Jeal goes further, and, in Chapter Two of his biography, subjects Stanley's account in his posthumously published Autobiography to detailed analysis. Because Stanley got so many basic facts wrong about his 'adoptive' family, Jeal concludes that it is very unlikely that he ever met rich Henry Hope Stanley, and that an ordinary grocer, James Speake, was Rowlands' true benefactor until his (Speake's) sudden death in October 1859.

In 1874, the New York Herald and Britain's Daily Telegraph financed Stanley on another expedition to Africa. His objective was nothing less than to complete the exploration and mapping of the central African lakes and rivers, in the process circumnavigating Lakes Victoria and Tanganyika and locating the source of the Nile. Between 1875 and 1876 Stanley succeeded in the first part of his objective, establishing that Lake Victoria had only a single outlet – the one located by John Hanning Speke on 21 July 1862. If this was not the Nile's source, then the massive northward flowing river called by Livingstone, the Lualaba, and mapped by him in its upper reaches, might flow on north to connect with the Nile via Lake Albert and thus be the primary source.

Following the Civil War, Stanley became a Journalist in the days of frontier expansion in the American West. He then organised an expedition to the Ottoman Empire that ended catastrophically when he was imprisoned. He eventually talked his way out of jail and received restitution for damaged expedition equipment. In 1867 Stanley offered his services to James Gordon Bennett Jr. of the New York Herald as a special correspondent with the British expeditionary force sent against Tewodros II of Ethiopia, and Stanley was the first to report the fall of Magdala in 1868. An assignment to report on the Spanish Civil War followed.

In 1869 Stanley received instructions to undertake a roving commission in the Middle East, which was to include the relief of Dr. David Livingstone, of whom little had been heard since his departure for Africa in 1866 to search for the source of the Nile.

Writer Tim Jeal has argued that during Stanley's 1871 expedition, he treated his indigenous porters well under contemporary standards. Three quarters of his African assistants on his third expedition had enlisted with him on an earlier journey.

The Herald's own first account of the meeting, published 1 July 1872, reports:

Richard Francis Burton, however, wrote that Stanley "shoots negroes as if they were monkeys". The remark was made in an 1873 letter to John Kirk, the British consul at Zanzibar. Separately in 1877, General Charles George Gordon remarked in a letter to Burton that Stanley shared Samuel Baker's tendency to publicise his own morally questionable actions: "These things may be done, but not advertised." On self-defence, Stanley wrote: "We went into the heart of Africa uninvited, therein lies our fault, but it was not so grave that our lives [when threatened] should be forfeited".

Stanley was approached by King Leopold II of Belgium, the ambitious Belgian monarch who had organized a private holding company in 1876 disguised as an international scientific and philanthropic association, which he called the International African Association. Soon after Stanley returned from the Congo, Leopold II tried to recruit him. Stanley, still hopeful for British backing, brushed him off. However, Leopold persisted and eventually Stanley gave in.

In 1877, Augustus Sparhawk, a trader with a United States company on Zanzibar, alleged in writing that John Kirk, who detested Stanley for blackening his character, had bribed two of Stanley's assistants, Manwa Sera and Kacheche, to tell missionaries and others that Stanley had behaved brutally in Africa.

Having established a beachhead on the lower Congo, in 1883 Stanley set out upriver to extend Leopold's domain, employing his usual methods: negotiations with local chiefs buying sovereignty in exchange for bolts of cloth and trinkets; playing one tribe off another or even shooting an obstructive chief and negotiating with his cowed successor instead. However, as he approached Stanley Falls at the junction between the Congo proper and the Lualaba, close to the general vicinity of Central Africa where he had found Livingstone six years before, it soon became clear that Stanley's men were not the only intruders.

In 1886, Stanley led the Emin Pasha Relief Expedition to "rescue" Emin Pasha, the governor of Equatoria in the southern Sudan. King Leopold II demanded that Stanley take the longer route via the Congo River, hoping to acquire more territory and perhaps even Equatoria After immense hardships and great loss of life, Stanley met Emin in 1888, charted the Ruwenzori Range and Lake Edward, and emerged from the interior with Emin and his surviving followers at the end of 1890. But this expedition tarnished Stanley's name because of the conduct of the other Europeans — British gentlemen and army officers. Army Major Edmund Musgrave Barttelot was shot by a carrier after behaving with extreme cruelty. James Sligo Jameson, heir to Irish whiskey manufacturer Jameson's, bought an 11-year-old girl and offered her to cannibals to document and Sketch how she was cooked and eaten. Stanley found out only when Jameson had died of fever.

Conrad, however, had spent six months of 1890 as a steamship captain on the Congo, years after Stanley had been there (1879-1884) and five years after Stanley had been recalled to Europe and ceased to be Leopold's chief agent in Africa. By 1890, forced labour was being used to coerce Africans into collecting rubber. However, when Stanley had been there, the inner tube for bicycle tyres had not yet been invented and so there was then little demand for rubber.

Stanley entered Parliament as a Liberal Unionist member for Lambeth North, serving from 1895 to 1900. He became Sir Henry Morton Stanley when he was made a Knight Grand Cross of the Order of the Bath in the 1899 Birthday Honours, in recognition of his Service to the British Empire in Africa. In 1890 he was given the Grand Cordon of the Order of Leopold by King Leopold II.

He died in London on 10 May 1904. At his funeral, he was eulogised by Daniel P. Virmar. His grave is in the churchyard of St Michael and All Angels' Church in Pirbright, Surrey, marked by a large piece of granite inscribed with the words "Henry Morton Stanley, Bula Matari, 1841–1904, Africa". Bula Matari translates as "Breaker of Rocks" or "Breakstones" in Kongo and was Stanley's name among locals in Congo. It can be translated as a term of endearment for, as the leader of Leopold's expedition, he commonly worked with the labourers breaking rocks with which they built the first modern road along the Congo River. Author Adam Hochschild suggested that Stanley understood it as a heroic epithet, but there is evidence that Nsakala, the man who originally coined it, had meant it humorously.

Stanley, much more familiar with the rigours of the African climate and the complexities of local politics than Leopold, who died in 1909 without ever setting foot in the Congo, persuaded his patron that the first step should be the construction of a wagon trail and a series of forts. Leopold agreed, and in deepest secrecy, Stanley signed a five-year contract at a salary of £1,000 a year and set off to Zanzibar under an assumed name. To avoid discovery, materials and workers were shipped in by various roundabout routes, and communications between Stanley and Leopold were entrusted to Colonel Maximilien Strauch.

Stanley and Livingstone, a 1939 film, stars Spencer Tracy as Stanley and Cedric Hardwicke as Livingstone.

The 1949 comedy film Africa Screams is the story of a dimwitted clerk named Stanley Livington, played by Lou Costello. He is mistaken for a famous African Explorer and recruited to lead a treasure hunt.

On his return to Europe, Stanley married Welsh Artist Dorothy Tennant. They adopted a child named Denzil who donated around 300 items to the Stanley archives at the Royal Museum of Central Africa in Tervuren, Belgium in 1954. He died in 1959.

Professor Norman R. Bennett of Boston University, who edited the 1970 book Stanley's Dispatches to the New York Herald, said the following in his introduction to the book: "Stanley remains one of the most controversial of the major European explorers of Africa. His often turbulent career and the internal stresses of his personality help to explain this fact. Nonetheless, there is no apparent reason why, more than three-quarters of a century after his last venture, Stanley should continue to be singled out for his supposed excesses in Africa, while other European explorers, often responsible for far more loss of life than Stanley, receive sympathetic treatment." For Example, Pierre Savorgnan de Brazza, who was revered in France, had shot Africans in self-defence but, unlike Stanley, never spoke of it. Samuel Baker killed far more Africans than Stanley did and, in 1873, was mauled in the press for "cold blooded murder". David Livingstone shot dead several African Yao slave traders in 1861, when they attacked the mission at Magomero.

In 1971, the BBC produced a six-part dramatised documentary series entitled Search for the Nile. Much of the series was shot on location, with Stanley played by Keith Buckley.

Stanley appears as a character in Simon Gray's 1978 play The Rear Column. The play tells the story of the men left behind to wait for Tippu Tib while Stanley went on to relieve Emin Pasha.

A Nintendo Entertainment System video game based on his life was released in 1992 called Stanley: The Search for Dr. Livingston.

In 1997, the made-for-television film Forbidden Territory: Stanley's Search for Livingstone was produced by National Geographic. Stanley was portrayed by Aidan Quinn, and Livingstone was portrayed by Nigel Hawthorne.

In 2004, Welsh Journalist Tim Butcher wrote his book Blood River: A Journey to Africa's Broken Heart. The book followed Stanley's journey through the Congo.

The 2009 History Channel series Expedition Africa documented a group of explorers attempting to traverse the route of Stanley's expedition in search of Livingstone.

In 2015, Oscar Hijuelos's novel Twain & Stanley Enter Paradise retold the story of Stanley's life through a focus on his friendship with Mark Twain.

Tippu Tip, the most powerful of Zanzibar's slave traders of the 19th century, was well-known to Stanley, as was the social chaos and devastation brought by slave-hunting. It had only been through Tippu Tip's help that Stanley had found Livingstone, who had survived years on the Lualaba by virtue of Tippu Tip's friendship. Now, Stanley discovered that Tippu Tip's men had reached still further west in search of fresh populations to enslave.