Jean-Paul Marat was born in Boudry in the Prussian principality of Neuchâtel, now part of Switzerland, on 24 May 1743. He was the second of nine children born to Jean Mara (Giovanni Mara), a native of Cagliari, Sardinia, and Louise Cabrol, a French Huguenot from Castres. His father was a Mercedarian "commendator" and religious refugee who converted to Calvinism in Geneva. At the age of sixteen, Marat left home and set off in search of fame and fortune, aware of the limited opportunities for outsiders. His highly educated father had been turned down for several secondary teaching posts. His first post was as a private tutor to the wealthy Nairac family in Bordeaux. After two years there he moved on to Paris where he studied medicine without gaining any formal qualifications. Moving to London around 1765, for fear of being "drawn into dissipation", he set himself up informally as a doctor, befriended the Royal Academician artist Angelika Kauffmann, and began to mix with Italian artists and architects in the coffee houses around Soho. Highly ambitious, but without patronage or qualifications, he set about imposing himself into the intellectual scene with essays on philosophy ("A philosophical Essay on Man", published 1773) and political theory ("Chains of Slavery", published 1774). Voltaire's sharp critique in defense of his friend Helvétius brought the young Marat to wider attention for the first time and reinforced his growing sense of the wide division between the materialists, grouped around Voltaire on one hand, and their opponents, grouped around Rousseau on the other.

Around 1770, Marat moved to Newcastle upon Tyne, possibly gaining employment as a veterinarian. His first political work Chains of Slavery, inspired by the activities of the MP and Mayor John Wilkes, was most probably compiled in the central library here. By Marat's own colourful account, he lived on black coffee for three months, during its composition, sleeping only two hours a night - and then slept soundly for thirteen days in a row. He gave it the subtitle, "A work in which the clandestine and villainous attempts of Princes to ruin Liberty are pointed out, and the dreadful scenes of Despotism disclosed". It earned him honorary membership of the patriotic societies of Berwick, Carlisle and Newcastle. The Newcastle Literary and Philosophical Society Library possesses a copy, and Tyne and Wear Archives Service holds three presented to the various Newcastle guilds.

A published essay on curing a friend of gleets (gonorrhea) probably helped him to secure his referees for an honorary medical degree from the St. Andrews University in June 1775. On his return to London, he further enhanced his reputation with the publication of an Enquiry into the Nature, Cause, and Cure of a Singular Disease of the Eyes.

In 1776, Marat moved to Paris following a brief stopover in Geneva to visit his family. Here his growing reputation as a highly effective doctor, along with the patronage of the marquis de l'Aubespine, the husband of one of his patients, secured his appointment, in 1777, as physician to the bodyguard of the comte d'Artois, Louis XVI's youngest brother who was to become king Charles X in 1824. The position paid 2,000 livres a year plus allowances. Marat was soon in great demand as a court doctor among the aristocracy and he used his new-found wealth to set up a laboratory in the marquise de l'Aubespine's (thought to be his mistress) house. Soon he was publishing works on fire & heat, electricity and light. In his Mémoires, his later enemy Brissot admitted Marat's growing influence in Parisian scientific circles. However, when Marat presented his scientific researches to the Académie des Sciences, they were not approved and he was rejected as a member several times. In particular, the Academicians were appalled by his temerity in disagreeing with the (hitherto uncriticized) Newton. Benjamin Franklin visited him on several occasions and Goethe described his rejection by the Academy as a glaring example of scientific despotism. In 1780, Marat published his "favourite work", a Plan de législation criminelle. Inspired by Rousseau and Beccaria, his polemic for judicial reform argued for a common death penalty for all regardless of social class and the necessity for a twelve-man jury to ensure fair trials.

In April 1786, he resigned his court appointment and devoted his energies full-time to scientific research. He published a well received translation of Newton's Opticks (1787), and later a collection of experimental essays including a study on the effect of light on soap bubbles in his Mémoires académiques, ou nouvelles découvertes sur la lumière ("Academic memoirs, or new discoveries on light", 1788).

On the eve of the French Revolution, Marat placed his career as a scientist and doctor behind him and took up his pen on behalf of the Third Estate. After 1788, when the Parlement of Paris and other Notables advised the assembling of the Estates-General for the first time in 175 years, Marat devoted himself entirely to politics. His Offrande à la Patrie ("Offering to the Nation") dwelt on much the same points as the Abbé Sieyès' famous "Qu'est-ce que le Tiers État?" ("What is the Third Estate?") When the Estates-General met, in June 1789, he published a supplement to his Offrande, followed in July by La Constitution ("The Constitution") and in September by the Tableau des vices de la constitution d'Angleterre ("Tableau of the flaws of the English constitution") intended to influence the structure of a constitution for France. The latter work was presented to the National Constituent Assembly and was an anti-oligarchic dissent from the anglomania that was gripping that body.

In September 1789, Marat began his own paper, which was at first called Moniteur patriote ("Patriotic Watch"), changed four days later to Publiciste parisien, and then finally L'Ami du peuple ("The Friend of the People"). From this position, he expressed suspicion of those in power, and dubbed them "enemies of the people". Although Marat never joined a specific faction during the Revolution, he condemned several sides in his L'Ami du peuple, and reported their alleged disloyalties (until he was proven wrong or they were proven guilty). Marat often attacked the most influential and powerful groups in Paris, including the Corps Municipal, the Constituent Assembly, the ministers, and the Cour du Châtelet. In January 1790, he moved to the radical Cordeliers section, the Club des Cordeliers, then under the leadership of the lawyer Danton, was nearly arrested for his aggressive campaign against the marquis de La Fayette, and was forced to flee to London, where he wrote his Dénonciation contre Necker ("Denunciation of Jacques Necker"), an attack on Louis XVI's popular Finance Minister. In May, he returned to Paris to continue the publication of L'Ami du peuple, and attacked many of France's most powerful citizens. Fearing reprisal, Marat went into hiding in the Paris sewers, where he almost certainly aggravated a debilitating chronic skin disease (dermatitis herpetiformis). During this period, Marat made regular attacks on the more conservative revolutionary leaders. In a pamphlet from 26 July 1790, entitled "C'en est fait de nous" ("We're done for!"), he wrote:

From 1790 to 1792, Marat frequently had to go into hiding. In April 1792, he married the 26-year-old Simonne Evrard in a common law ceremony on his return from exile in London, having previously expressed his love for her. She was the sister-in-law of his typographer, Jean-Antoine Corne, and had lent him money and sheltered him on several occasions.

Marat only emerged publicly on the 10 August Insurrection, when the Tuileries Palace was invaded and the royal family forced to shelter within the Legislative Assembly. The spark for this uprising was Karl Wilhelm Ferdinand, Duke of Brunswick-Luneburg's provocative proclamation, which called for the crushing of the Revolution and helped to inflame popular outrage in Paris.

Marat was elected to the National Convention in September 1792 as one of 26 Paris deputies although he belonged to no party. When France was declared a Republic on 22 September, Marat renamed his L'Ami du peuple as Le Journal de la République française ("Journal of the French Republic"). His stance during the trial of the deposed king Louis XVI was unique. He declared it unfair to accuse Louis for anything before his acceptance of the French Constitution of 1791, and, although implacably believing that the monarch's death would be good for the people, defended Guillaume-Chrétien de Lamoignon de Malesherbes, the King's counsel, as a "sage et respectable vieillard" ("wise and respected old man").

On 21 January 1793, Louis XVI was guillotined, which caused political turmoil. From January to May, Marat fought bitterly with the Girondins, whom he believed to be covert enemies of republicanism. The Girondins won the first round when the Convention ordered that Marat should be tried before the Revolutionary Tribunal. However, their plans were scuppered when Marat was acquitted with much popular support and carried back to the Convention in triumph with a greatly enhanced public profile. The fall of the Girondins on 2 June, helped by the actions of François Hanriot, the new leader of the National Guard, was one of Marat's last great achievements. Forced to retire from the Convention as a result of his worsening skin disease, he continued to work from home, where he soaked in a medicinal bath. Now that The Mountain no longer needed his support in the struggle against the Girondins, Robespierre and other leading Montagnards began to separate themselves from him, while the Convention largely ignored his letters.

Marat was in his bathtub on 13 July, when a young woman from Caen, Charlotte Corday, appeared at his flat, claiming to have vital information on the activities of the escaped Girondins who had fled to Normandy. Despite his wife Simonne's protests, Marat asked for her to enter and gave her an audience by his bath, over which a board had been laid to serve as a writing desk. Their interview lasted around fifteen minutes. He asked her what was happening in Caen and she explained, reciting a list of the offending deputies. After he had finished writing out the list, Corday claimed that he told her, "Their heads will fall within a fortnight". A statement which she later changed at her trial to, "Soon I shall have them all guillotined in Paris". This was unlikely since Marat did not have the power to have anyone guillotined. At that moment, Corday rose from her chair, drawing out the eight-inch kitchen knife concealed in her corset, which she had bought earlier that day, and brought it down hard into Marat’s chest, where it pierced his ribs, perforating the right lung and severing the aorta, close to the heart. The massive bleeding was fatal within seconds. Slumping backwards, Marat cried out his last words to Simonne, "À moi, ma chère amie!" ("Help me, my dear friend!") and died.

Corday was a Girondin sympathiser who came from an impoverished royalist family — her brothers were émigrés who had left to join the exiled royal princes. From her own account, and those of witnesses, it is clear that she had been inspired by Girondin speeches to a hatred of the Montagnards and their excesses, symbolised most powerfully in the character of Marat. Marat's assassination contributed to the mounting suspicion which fed the Terror during which thousands of the Jacobins' adversaries – both royalists and Girondins – were executed on supposed charges of treason. Charlotte Corday was guillotined on 17 July 1793 for the murder. During her four-day trial, she had testified that she had carried out the assassination alone, saying "I killed one man to save 100,000."

Marat's assassination led to his apotheosis. The painter Jacques-Louis David, a member of one of the two 'Great Committees' (the Committee of General Security), was asked to organize a grand funeral. David took up the task of immortalizing Marat in the painting The Death of Marat, beautifying the skin that was discoloured and scabbed from his chronic skin disease in an attempt to create antique virtue. The entire National Convention attended Marat's funeral and he was buried under a weeping willow, in the garden of the former Club des Cordeliers (former Couvent des Cordeliers). On his tomb, the inscription on a plaque read: "'Unité, Indivisibilité de la République, Liberté, Égalité, Fraternité ou la mort'". His heart was embalmed separately and placed in an urn in an altar erected to his memory at the Cordeliers. His remains were transferred to the Panthéon on 25 November 1793 and his near messianic role in the Revolution was confirmed with the elegy: Like Jesus, Marat loved ardently the people, and only them. Like Jesus, Marat hated kings, nobles, priests, rogues and, like Jesus, he never stopped fighting against these plagues of the people. The eulogy was given by the Marquis de Sade, delegate of the Section Piques and an ally of Marat's faction in the National Convention. By this stage De Sade was becoming disgusted with the excesses of the Reign of Terror and was later removed from office and imprisoned for "moderatism" on the fifth of December.

On 19 November, the port city of Le Havre-de-Grâce changed its name to Le Havre-de-Marat and then Le Havre-Marat. When the Jacobins started their dechristianisation campaign to set up the Cult of Reason of Hébert and Chaumette and Cult of the Supreme Being of Robespierre, Marat was made a quasi-saint, and his bust often replaced crucifixes in the former churches of Paris. By early 1795, however, Marat's memory had become tarnished. On 13 January 1795, Le Havre-Marat became simply Le Havre, the name it bears today. In February, his coffin was removed from the Panthéon and his busts and sculptures were destroyed. His final resting place is the cemetery of the Church Saint-Étienne-du-Mont.

His memory lived on in the Soviet Union. Marat became a common name and the Russian battleship Petropavlovsk (Russian: Петропавловск) was renamed Marat in 1921. A street in the centre of Sevastopol was named after Marat (Russian: Улица Марата) on 3 January 1921, shortly after the Soviets took over the city.

Described during his time as a man "short in stature, deformed in person, and hideous in face," Marat has long been noted for physical irregularities. The nature of Marat's debilitating skin disease, in particular, has been an object of ongoing medical interest. Dr. Josef E. Jelinek noted that his skin disease was intensely itchy, blistering, began in the perianal region, and was associated with weight loss leading to emaciation. He was sick with it for the three years prior to his assassination, and spent most of this time in his bathtub. There were various minerals and medicines that were present in his bath while he soaked to help ease the pain caused by his debilitating skin disease. The bandana that is seen wrapped around his head was soaked in vinegar to reduce the severity of his discomfort. Jelinek's diagnosis is dermatitis herpetiformis.

After Marat's death, his wife may have sold his bathtub to her journalist neighbour, as it was included in an inventory of his possessions after his death. The royalist de Saint-Hilaire bought the tub, taking it to Sarzeau, Morbihan in Brittany. His daughter, Capriole de Saint-Hilaire inherited it when he died in 1805 and she passed it on to the Sarzeau curé when she died in 1862. A journalist for Le Figaro tracked down the tub in 1885. The curé then discovered that selling the tub could earn money for the parish, yet the Musée Carnavalet turned it down due to its lack of provenance as well as the high price. The curé approached Madame Tussaud's waxworks, who agreed to purchase Marat's bathtub for 100,000 francs; however, the curé's acceptance was lost in the mail. After rejecting other offers, including one from Phineas Barnum, the curé sold the tub for 5,000 francs to the Musée Grévin, where it remains today. The tub was in the shape of an old-fashioned high-buttoned shoe and had a copper lining.