His formal education began in 1897 at Oxford Preparatory School (now Dragon School), where he gained a First Scholarship in 1904 to Eton. In 1905 he joined Eton, where he experienced severe abuse from senior students for allegedly being arrogant. The indifference of authority left him with a lasting hatred for the English education system. However, the ordeal did not stop him from becoming Captain of the school. He studied mathematics and classics at New College at the University of Oxford and obtained first-class honours in mathematical moderations in 1912 and first-class honours in Greats in 1914. He became engrossed in genetics and presented a paper on gene linkage in vertebrates in the summer of 1912. His first technical paper, a 30-page long article on haemoglobin function, was published that same year, as a co-author alongside his Father.

He grew up at 11 Crick Road, North Oxford. He learnt to read at the age of three, and at four, after injuring his forehead he asked the Doctor, "Is this oxyhaemoglobin or carboxyhaemoglobin?". From age eight he worked with his Father in their home laboratory where he experienced his first self-experimentation, the method he would later be famous for. He and his Father became their own "human guinea pigs", such as in their investigation on the effects of poison gases. In 1899 his family moved to "Cherwell", a late Victorian house at the outskirts of Oxford with its own private laboratory.

With his sister Naomi Mitchison, Haldane started investigating Mendelian genetics in 1908, used guinea pigs and mice, publishing Reduplication in mice in 1915 the first demonstration of genetic linkage in mammals, (As the paper was written during Haldane's Service in the First World War, James F. Crow called it "the most important science article ever written in a front-line trench.) He demonstrated the same phenomenon in chickens in 1921.

His education was interrupted by the First World War during which he fought in the British Army, being commissioned a temporary second lieutenant in the 3rd Battalion of the Black Watch (Royal Highland Regiment) on 15 August 1914. He was promoted to temporary lieutenant on 18 February 1915 and to temporary captain on 18 October. He served in France and Iraq, where he was wounded. He relinquished his commission on 1 April 1920, retaining his rank of captain. For his ferocity and aggressiveness in battles, his commander called him the "bravest and dirtiest officer in my Army."

His first paper in 1915 demonstrated genetic linkage in mammals while subsequent works helped to create population genetics, thus establishing a unification of Mendelian genetics and Darwinian evolution by natural selection whilst laying the groundwork for modern evolutionary synthesis. His article on abiogenesis in 1929 introduced the "primordial soup theory", and it became the foundation to build physical Models for the chemical origin of life. Haldane established human gene maps for haemophilia and colour blindness on the X chromosome, and codified Haldane's rule on sterility in the heterogametic sex of hybrids in species. He correctly proposed that sickle-cell disease confers some immunity to malaria. He was the first to suggest the central idea of in vitro fertilisation, as well as concepts such as: the hydrogen economy, cis and trans-acting regulation, coupling reaction, molecular repulsion, the darwin (as a unit of evolution) and organismal cloning. In 1957 he articulated Haldane's dilemma, a limit on the speed of beneficial evolution which subsequently proved incorrect. He willed his body for medical studies, as he wanted to remain useful even in death.

Between 1919 and 1922 he was a Fellow of New College, Oxford, where he researched physiology and genetics. He then moved to the University of Cambridge, where he accepted a readership in Biochemistry and taught until 1932. From 1927 until 1937 he was also Head of Genetical Research at the John Innes Horticultural Institution. During his nine years at Cambridge, Haldane worked on enzymes and genetics, particularly the mathematical side of genetics. He was the Fullerian Professor of Physiology at the Royal Institution from 1930 to 1932 and in 1933 he became full Professor of Genetics at University College London, where he spent most of his academic career. Four years later he became the first Weldon Professor of Biometry at University College London.

In 1923, in a talk given in Cambridge titled "Science and the Future", Haldane, foreseeing the exhaustion of coal for power generation in Britain, proposed a network of hydrogen-generating windmills. This is the first proposal of the hydrogen-based renewable Energy economy.

In 1924, Haldane met Charlotte Franken. So that they could marry, Charlotte divorced her husband, Jack Burghes, causing some controversy. Haldane was almost dismissed from Cambridge for the way he handled his meeting with her. They married in 1926. Following their separation in 1942, the Haldanes divorced in 1945. He later married Helen Spurway.

In 1925, with G. E. Briggs, Haldane derived a new interpretation of the enzyme kinetics law described by Victor Henri in 1903, different from the 1913 Michaelis–Menten equation. Leonor Michaelis and Maud Menten assumed that enzyme (catalyst) and substrate (reactant) are in fast equilibrium with their complex, which then dissociates to yield product and free enzyme. The Briggs–Haldane equation was of the same algebraic form; but their derivation is based on the quasi-steady state approximation, which is the concentration of intermediate complex (or complexes) does not change. As a result, the microscopic meaning of the "Michaelis Constant" (K_m) is different. Although commonly referring to it as Michaelis–Menten kinetics, most of the current Models typically use the Briggs–Haldane derivation.

Haldane introduced the modern concept of abiogenesis in an eight-page article titled The origin of life in the Rationalist Annual in 1929, describing the primitive ocean as a "vast chemical laboratory" containing a mixture of inorganic compounds – like a "hot dilute soup" in which organic compounds could have formed. Under the solar Energy the anoxic atmosphere containing carbon dioxide, ammonia and water vapour gave rise to a variety of organic compounds, "living or half-living things". The first molecules reacted with one another to produce more complex compounds, and ultimately the cellular components. At some point a kind of "oily film" was produced that enclosed self-replicating nucleic acids, thereby becoming the first cell. J. D. Bernal named the hypothesis biopoiesis or biopoesis, the process of living matter spontaneously evolving from self-replicating but lifeless molecules. Haldane further hypothesised that viruses were the intermediate entities between the prebiotic soup and the first cells. He asserted that prebiotic life would have been "in the virus stage for many millions of years before a suitable assemblage of elementary units was brought together in the first cell." The idea was generally dismissed as "wild speculation". In 1924 Alexander Oparin had suggested a similar idea in Russian, and in 1936 he introduced it to the English-speaking people. The experimental basis of the theory began in 1953 with the classic Miller–Urey experiment. Since then, the primordial soup theory became a dominant theory in the chemistry of life, and has been called the Oparin–Haldane hypothesis.

Haldane was elected a Fellow of the Royal Society in 1932. The French Government conferred him its National Order of the Legion of Honour in 1937. In 1952, he received the Darwin Medal from the Royal Society. In 1956, he was awarded the Huxley Memorial Medal of the Anthropological Institute of Great Britain. He received the Feltrinelli Prize from Accademia Nazionale dei Lincei in 1961. He also received an Honorary Doctorate of Science, an Honorary Fellowship at New College, and the Kimber Award of the US National Academy of Sciences. He was awarded the Linnean Society of London's prestigious Darwin–Wallace Medal in 1958.

Along with Olaf Stapledon, Charles Kay Ogden, I. A. Richards, and H. G. Wells, Haldane was accused by C. S. Lewis of scientism. Haldane criticised Lewis and his Ransom Trilogy for the "complete mischaracterisation of science, and his disparagement of the human race". He wrote a book for children titled My Friend Mr Leakey (1937), containing the stories "A Meal With a Magician", "A Day in the Life of a Magician", "Mr Leakey's Party", "Rats", "The Snake with the Golden Teeth", and "My Magic Collar Stud"; later editions featured illustrations by Quentin Blake. Haldane edited Gary Botting's manuscript on the genetics of giant silk moths with margin notes.

In 1938, he proclaimed enthusiastically that "I think that Marxism is true." He joined the Communist Party of Great Britain in 1942. He was pressed to speak out about the rise of Lysenkoism and the persecution of geneticists in the Soviet Union as anti-Darwinist and the denouncement of genetics as incompatible with dialectical materialism. He shifted the focus to the United Kingdom and a criticism of the dependence of scientific research on financial patronage. In 1941 he wrote about the Soviet trial of his friend and fellow Geneticist Nikolai Vavilov:

In 1949, Haldane proposed that genetic disorders in humans living in malaria-endemic regions provided a phenotype with immunity to blood-borne haemophiles. He noted that mutations expressed in red blood cells, such as sickle-cell anemia and various thalassemias, were prevalent only in tropical regions where malaria has been endemic. He further observed that these were favourable traits for natural selection which protected individuals from receiving malarial infection. This concept of resistance to malaria was eventually confirmed by Anthony C. Allison in 1954.

By the end of the Second World War Haldane had become an explicit critic of the regime. He left the party in 1950, shortly after considering standing for Parliament as a Communist Party candidate. He continued to admire Joseph Stalin, describing him in 1962 as "a very great man who did a very good job".

In 1956, Haldane left University College London, and joined the Indian Statistical Institute (ISI) in Kolkata, India, where he headed the biometry unit. Officially he stated that he left the UK because of the Suez Crisis, writing: "Finally, I am going to India because I consider that recent acts of the British Government have been violations of international law." He believed that the warm climate would do him good, and that India shared his socialist dreams. The university had sacked his wife Helen for excessive drinking and refusing to pay a fine, triggering Haldane's resignation. He declared he would no longer wear socks, "Sixty years in socks is enough." and always dressed in Indian attire.

Haldane became an Indian citizen. He was also interested in Hinduism and became a vegetarian. In 1961, Haldane described India as "the closest approximation to the Free World." Jerzy Neyman objected that "India has its fair share of scoundrels and a tremendous amount of poor unthinking and disgustingly subservient individuals who are not attractive." Haldane retorted:

When on 25 June 1962 he was described in print as a "Citizen of the World" by Groff Conklin, Haldane's response was as follows:

Haldane was the first to have thought of the genetic basis for the cloning of humans, and eventually super-talented individuals. For this he coined the term "clone", though the synonym "clon" (from the Greek word klon meaning "twig") had been used in horticulture since the 19th century. He introduced the term in his speech on "Biological Possibilities for the Human Species of the Next Ten Thousand Years" at the Ciba Foundation Symposium on Man and his Future in 1963.

Haldane died on 1 December 1964. He willed that his body be used for study at the Rangaraya Medical College, Kakinada.