He was born at Providence Green, Green Hammerton, near Harrogate, Yorkshire, the youngest son of Samuel Jackson, a yeoman who owned and farmed his land, and the former Sarah Hughlings, the daughter of a Welsh revenue collector. His mother died just over a year after giving birth to him. He had three brothers and a sister; his brothers emigrated to New Zealand and his sister married a physician. He was educated at Tadcaster, Yorkshire, and Nailsworth, Gloucestershire, before attending the York Medical and Surgical School. After qualifying at St Barts in 1856 he became house physician to the York Dispensary.

In 1859 he returned to London to work at the Metropolitan Free Hospital and the London Hospital. In 1862 he was appointed Assistant Physician, later (1869) full Physician at the National Hospital for Paralysis and Epilepsy located in Queen Square, London (now the National Hospital for Neurology and Neurosurgery) as well as Physician (1874) at the London Hospital. During this period he established his reputation as a neurologist. He was elected a Fellow of the Royal Society in 1878.

Jackson died in London on 7 October 1911 and was buried in Highgate cemetery.

Jackson was an innovative thinker and a prolific and lucid, if sometimes repetitive, writer. Though his range of interests was wide, he is best remembered for his seminal contributions to the diagnosis and understanding of epilepsy in all its forms and complexities. His name is attached eponymously to the characteristic "march" of symptoms in focal motor seizures and to the so-called "dreamy state" of psychomotor seizures of temporal lobe origin. His papers on the latter variety of epilepsy have seldom been bettered in their descriptive clinical detail or in their analysis of the relationship of psychomotor epilepsy to various patterns of pathological automatism and other mental and behavioural disorders.

In his youth Jackson had been interested in conceptual issues and it is believed that in 1859 he contemplated the idea of abandoning medicine for philosophy. Thus, an important part of his work concerned the evolutionary organization of the nervous system for which he proposed three levels: a lower, a middle, and a higher. At the lowest level, movements were to be represented in their least complex form; such centres lie in the medulla and spinal cord. The middle level consists of the so-called motor area of the cortex, and the highest motor levels are found in the prefrontal area.

The higher centres inhibited the lower ones and hence lesions thereat caused ‘negative’ symptoms (due to an absence of function). ‘Positive’ symptoms were caused by the functional release of the lower centres. This process Jackson called ‘dissolution’, a term he borrowed from Herbert Spencer. The ‘positive - negative’ distinction he took from Sir John Reynolds.

Continental psychiatrists and psychologists (e.g. Ribot, Janet, Freud, Ey) have been more influenced by Jackson’s theoretical ideas than their British counterparts. During the 1980s, the ‘positive - negative’ distinction was temporarily fashionable in relation to the symptoms of schizophrenia.

He was one of only a few physicians to have delivered the Goulstonian (1869), Croonian (1884) and Lumleian (1890) lectures to the Royal College of Physicians  He also delivered the 1872 Hunterian Oration to the Hunterian Society.

Jackson could not use modern sophisticated neuro - investigative technology (it had not been invented), but had to rely upon his own powers of clinical observation and deductive logic. Some of his eminent successors in the field of British neurology have been critical of many of his theories and concepts; but as Sir Francis Walshe remarked of his work in 1943, " ... when all that is obsolete or irrelevant is discarded there remains a rich treasure of physiological insight we cannot afford to ignore."

In Otfrid Foerster's research on the motor cortex, he cites exclusively Hughlings Jackson for the initial discovery (although without evidence) of the brain as the spring of neurological motor signaling.

Together with his friends Sir David Ferrier and Sir James Crichton - Browne, two eminent neuropsychiatrists of his time, Jackson was one of the founders of the important Brain journal, which was dedicated to the interaction between experimental and clinical neurology (still being published today). Its inaugural issue came to light in 1878.

In 1892, Jackson was one of the founding members of the National Society for the Employment of Epileptics (now the National Society for Epilepsy), along with Sir William Gowers and Sir David Ferrier.

Oliver Sacks has repeatedly cited Jackson as an inspiration in his neurologic work.