Stopes was born in Edinburgh. Her Father, Henry Stopes, was a brewer, Engineer, Architect and Paleontologist from Colchester. Her mother was Charlotte Carmichael Stopes, a Shakespearean scholar and women's rights campaigner from Edinburgh. At six weeks old, her parents took Stopes from Scotland; the family stayed briefly in Colchester then moved to London, where in 1880 her Father bought 28 Cintra Park in Upper Norwood. Both of her parents were members of the British Association for the Advancement of Science, where they had met. Marie was taken to meetings where she met the famous scholars of the day. At first, she was home-schooled, but from 1892 to 1894 she attended St George's School for Girls in Edinburgh. Stopes was later sent to the North London Collegiate School, where she was a close friend of Olga Fröbe-Kapteyn.

Stopes attended University College, London as a scholarship student, where she studied botany and geology; she graduated with a first class B.Sc. in 1902 after only two years by attending both day and night schools. Following this, Stopes earned a D.Sc. degree from University College London, becoming the youngest person in Britain to have done so. In 1903 she published a study of the botany of the recently dried-up Ebbsfleet River. After carrying out research on Carboniferous plants at the Royal Botanic Gardens, Kew, and at University College, London, she studied the reproduction of living cycads at the University of Munich, receiving a Ph.D. in botany in 1904. Also in 1904, she was one of the first women to be elected a fellow of the Linnean Society of London. She was also Fellow and sometime Lecturer in Palaeobotany at University College, London until 1920. She held the post of Lecturer in Palaeobotany at the University of Manchester from 1904 to 1910; in this capacity she became the first female academic of that university.

Stopes had a relationship, mainly through correspondence, with Japanese Botanist Kenjiro Fujii, whom she met at the University of Munich in 1904 while researching her Ph.D. In 1907, during her 1904–1910 tenure at Manchester University, she arranged to research in Japan, allowing her to be with Fujii. The relationship ended.

In 1907, Stopes went to Japan on a scientific mission. She spent eighteen months at the Imperial University, Tokyo and explored coal mines on Hokkaido for fossilised plants. She published her Japanese experiences as a diary, called "Journal from Japan: a daily record of life as seen by a scientist", in 1910.

In 1910, the Geological Survey of Canada commissioned Stopes to determine the age of the Fern Ledges, a geological structure at Saint John, New Brunswick. It is part of the Early Pennsylvanian epoch Lancaster Formation. Canadian scholars were divided between dating it to the Devonian period or to the Pennsylvanian/Upper Carboniferous period. Stopes arrived in North America before Christmas to start her research. On 29 December, she met the Canadian researcher Reginald Ruggles Gates in St. Louis, Missouri; they became engaged two days later. Starting her work on the Fern Ledges in earnest in February 1911, she did geological field work and researched at geological collections in museums, and shipped specimens to England for further investigation. The couple married in March and returned to England on 1 April that year. Stopes continued her research. In mid-1912 she delivered her results, finding for the Pennsylvanian period of the Carboniferous. The Government of Canada published her results in 1914. Later the same year, her marriage to Gates was annulled.

Stopes attended the inaugural congress of the Eugenics Society in 1912 and became a fellow in 1921. The same year, she founded the Society for Constructive Birth Control and Racial Progress to "promote eugenic birth control", in part because "the Society refused to place birth control prominently on its platform". The Mother's Clinic was established in 1921 to further eugenic aims; it dispensed the so-called "Pro-Race" cervical cap. According to Historian Richard Soloway's The Galton Lecture in 1996:

In 1911, Stopes married Canadian Geneticist Reginald Ruggles Gates. She had maintained her name out of principle; her work was blooming while his was struggling. He was disturbed by what he considered her suffragette support. He failed to assert his position as head of the household and was frustrated. After another year, she sought legal advice about ending the marriage. Not receiving useful help, she read the legal code seeking a way to get a divorce. The marriage had fallen apart amid squabbling over the house and rent. On 11 May 1913, Stopes filed for divorce on the grounds that the marriage had never been consummated. Gates left England the following year and did not contest the divorce.

In 1917, before meeting Marie Stopes, Humphrey Roe offered to endow a birth control clinic attached to St Mary's Hospital in Manchester. He proposed all patients would be married and that no abortions would be done, but his offer was declined. This was a serious issue for Roe; after their marriage, he and Stopes planned to open a clinic for poor mothers in London.

In 1918 she married Humphrey Verdon Roe, the financial backer of her most famous work, Married Love: A New Contribution to the Solution of the Sex Difficulties. Their son, Harry Stopes-Roe, was born in 1924. Stopes disliked Harry's companion, Mary Eyre Wallis, who was the daughter of the noted Engineer Barnes Wallis. When Harry announced their engagement in October 1947, his mother set about "to try to sabotage the union". She found fault with Mary and wrote to Mary's Father to complain. She tried to get Humphrey's support against the marriage, arguing that any grandchildren might inherit Mary's myopia. He was not persuaded. Later, believing "he had betrayed her by this marriage", Stopes cut him out of any substantial inheritance.

On 16 July 1919, Stopes—pregnant and a month overdue—entered a nursing home. Stopes and the doctors clashed over the method of birth—she was not allowed to give birth on her knees. The child was stillborn; the doctors suggested the incident was due to syphilis, but an examination excluded the possibility. Stopes was furious and said her baby had been murdered. She was 38 years old.

Stopes also campaigned to get eugenic ideas adopted by those in power. In 1920, she sent a copy of "Radiant Motherhood" to Prime Minister Lloyd George's secretary and drew attention to the chapter on eugenics (Chapter XX) In 1922, she sent a declaration to the candidates in the upcoming parliamentary election, asking them to sign it. It read:

Stopes became enthusiastic about a contraceptive device called the "gold pin", which was reportedly successful in America. A few months later, she asked Norman Haire, a young Australian Doctor, whether he would be interested in running a clinical trial of the device, as she had two correspondents who wanted to use it. Haire had already investigated the device and found it to be dangerous. Haire became involved in another birth control clinic that opened in Walworth in November 1921; later a rivalry between Stopes and Haire erupted in The Lancet. Haire brought up the gold-pin episode, even though Stopes' clinic had never used it. The issue of the gold pin device resurfaced in the Stopes-Sutherland libel case a few years later.

In 1922, Dr Halliday Sutherland wrote a book called Birth Control: A Statement of Christian Doctrine Against the Neo Malthusians. In the inter-war years, the terms "birth control" and "eugenics" were closely related; according to Jane Carey they were "so intertwined as to be synonymous".

In 1923, Marie Stopes bought the Old Higher Lighthouse on the Isle of Portland, Dorset, as an escape from the difficult climate of London during her court case against H. G. Sutherland. The island's Jurassic fossil forests provided her with endless interest. She founded and curated the Portland Museum, which opened in 1930. The cottage housing the museum was an inspiration behind The Well-Beloved, a novel by Thomas Hardy, who was a friend of Marie Stopes.

The judge ignored the general tenor of the jury's response and found in Sutherland's favour based on the response to #2. It was a moral victory for Stopes as the press saw it, and she appealed. On 20 July, the Court of Appeal reversed the previous decision, awarding the £100 to Stopes, but the Catholic community mobilised to support Sutherland — himself a Catholic — for a final appeal to the House of Lords on 21 November 1924. The Lords' irrevocable decision was in Sutherland's favour. The cost for Stopes was vast; but publicity and book sales partially compensated her losses. The trial had made birth control a public topic and the number of clients visiting the clinic doubled.

In 1925, the Mothers' Clinic moved to Central London, where it remains as of 2015. Stopes gradually built up a small network of clinics across Britain, working to fund them. She opened clinics in Leeds in April 1934; Aberdeen in October 1934; Belfast in October 1936; Cardiff in October 1937; and Swansea in January 1943.

Stopes wrote poems and plays; during the First World War she wrote increasingly didactic plays. Her first major success was Our Ostriches, a play that dealt with society's approach to working class women being forced to produce babies throughout their lives. The play ran for three months at the Royal Court Theatre. It was hurriedly produced in place of Vectia, another of Stopes' plays. Vectia is an autobiographical attempt to analyse the failure of Stopes' first marriage. Because of its themes of sex and impotence, it was denied a licence to be performed, despite Stopes's frequent efforts. In 1926, Stopes had Vectia printed under the title A Banned Play and a Preface on Censorship. None of her later plays reached the stage.

In 1935 Stopes attended the International Congress for Population Science in Berlin. She was more than once accused of being anti-Semitic by other pioneers of the birth control movement. During the Second World War, Stopes received a letter from friends whom she had invited to lunch asking whether they could bring with them a Jewish refugee from Nazi Germany in their care; Stopes replied they could not; it would offend her other guests.

According to Ruth Hall, Stopes wrote poetry expressing her anti-Prussian, anti-Catholic and anti-Russian views. In August 1939, Stopes sent a copy of her book Love Songs for Young Lovers to Adolf Hitler with the following cover letter:

She wanted her poems to be distributed through the German birth control clinics, but the letter has been interpreted as showing sympathy for Hitler. However, according to Rose, any sympathy she may have had would have dissipated when Hitler closed the clinics, whereas on 12 July 1940 she wrote to Winston Churchill to offer a slogan, "Fight the Battle of Britain in Berlin's Air".

Stopes died on 2 October 1958, aged 77, from breast cancer at her home in Dorking, Surrey. Her will left her clinic to the Eugenics Society; most of her estate went to the Royal Society of Literature. Her son Harry received her copy of the Greater Oxford Dictionary and other small items. An English Heritage blue plaque commemorates Stopes at 28 Cintra Park, Upper Norwood, where she lived from 1880 to 1892.

The clinics continued to operate after Stopes' death, but by the early 1970s they were in financial difficulties and in 1975 they went into voluntary receivership. Marie Stopes International was established a year later as an international non-governmental organisation (NGO) working on sexual and reproductive health. The global partnership took over responsibility for the main clinic, and in 1978 it began its work overseas in New Delhi, India. Since then the organisation has grown steadily; today it works in over forty countries, has 452 clinics and has offices in London, Brussels, Melbourne and in the US.

The free clinic was open to all married women for knowledge about reproductive health. Stopes opposed abortion; she tried to discover alternatives for families and increase knowledge about birth control and the reproductive system. Options included the cervical cap—which was the most popular—coitus interruptus, and spermicides based on soap and oil. Stopes rediscovered the use of olive oil-soaked sponges as an alternative birth control. Olive oil's use as a spermicide dates to Greek and Roman times. Her recipe proved very effective. She tested many of her contraceptives on patients at her clinics.