A year later, the family returned to Moscow, remaining there after Herzen had completed his studies at Moscow University. In 1834, Herzen and his lifelong friend Nikolay Ogarev were arrested and tried on charges of having attended a festival during which verses by Sokolovsky that were uncomplimentary to the tsar, were sung. He was found guilty, and in 1835 banished to Vyatka, now Kirov, in north-eastern Russia. He remained there until 1837, when the tsar's son, Grand Duke Alexander (later to become tsar Alexander II), accompanied by the poet Zhukovsky, visited the city and intervened on his behalf. Herzen was allowed to leave Vyatka for Vladimir, where he was appointed Editor of the city's official gazette. In 1837, he eloped with his cousin Natalya Zakharina, secretly marrying her.

In 1839 he was set free and returned to Moscow in 1840, where he met literary critic Vissarion Belinsky, who was strongly influenced by him. Upon arrival he was appointed as secretary to Count Strogonoff in the ministry of the interior at St Petersburg; but as a consequence of complaining about a death caused by a police officer, was sent to Novgorod, where he was a state councillor until 1842. In 1846, his Father died, leaving him a large amount of property.

His literary career began in 1842 with the publication of an essay, in Russian, on Dilettantism in Science, under the pseudonym of Iskander, the Turkish form of his Christian name. His second work, also in Russian, was his Letters on the Study of Nature (1845–46). In 1847 appeared his novel Who is to blame? This is a story about how the domestic happiness of a young tutor, who marries the unacknowledged daughter of a Russian sensualist of the old type, dull, ignorant and genial, is troubled by a Russian sensualist of the new school, intelligent, accomplished, and callous, with there being no possibility of saying who is most to blame for the tragic ending.

Also in 1847 were published in Russian periodicals the stories which were afterwards collected and printed in London in 1854, under the title of Prervannye Razskazy (Interrupted Tales). In 1850 two works appeared, translated from the Russian manuscripts, From Another Shore and Lettres de France et d'Italie. In French also appeared his essay Du Developpement des idées revolutionnaires en Russie, and his Memoirs, which, after being printed in Russian, were translated under the title of Le Monde russe et la Révolution (3 vols., 1860–1862), and were in part translated into English as My Exile to Siberia (2 vols., 1855).

Herzen was disillusioned with the Revolutions of 1848 but not disillusioned with revolutionary thought. He became critical of those 1848 Revolutionaries who were "so revolted by the Reaction after 1848, so exasperated by everything European, that they hastened on to Kansas or California". Herzen had always admired the French Revolution and broadly adopted its values. In his early writings, he viewed the French Revolution as the end of history, the final stage in social development of a society based on humanism and harmony. Throughout his early life, Herzen saw himself as a revolutionary radical called to fight the political oppression of Nicholas I of Russia. Essentially, Herzen fought against the ruling elites in Europe, against Christian hypocrisy and for individual freedom and self-expression.

Herzen and his wife Natalia had four children together. His mother and one of his sons died in a shipwreck in 1851. His wife carried on an affair with the German poet Georg Herwegh and died from tuberculosis in 1852. That same year, Herzen left Geneva for London, where he settled for many years. He hired Malwida von Meysenbug to educate his daughters. With the publications of his Free Russian Press, which he founded in London in 1853, he attempted to influence the situation in Russia and improve the situation of the Russian peasantry he idolized.

Having founded in London in 1853 his Free Russian Press, the fortunes of which he gave an interesting account in a book published (in Russian) in 1863, he published a large number of Russian works, all against the system of government prevailing in Russia. Some of these were essays, such as his Baptized Property (1853), an attack on serfdom; others were periodical publications, the Polyarnaya Zvyezda (or Polar Star), the Kolokol (or Bell), and the Golosa iz Rossii (or Voices from Russia).

The year 1855 gave Herzen reason to be optimistic; Alexander II had ascended the throne and reforms seemed possible. Herzen urged the Tsarist regime 'Onward, onward' towards reform in The Polar Star in 1856. Writing in 1857 Herzen became excited by the possibility of social change under Alexander II, "A new life is unmistakably boiling up in Russia, even the government is being carried away by it". The Bell broke the story that the government was considering serf emancipation in July 1857, adding that the government lacked the ability to resolve the issue. Yet by 1858, full serf emancipation had not been achieved and Herzen grew impatient with reform. By May 1858 The Bell restarted its campaign to for the comprehensive emancipation of the serfs. Once the Emancipation reform of 1861 in Russia was achieved, The Bell's campaign changed to 'Liberty and Land', a program that tried to achieve further social change in support of serf rights. Alexander II granted serfs their freedom, the law courts were remodelled, trial by jury was established, and liberty was, to a great extent, conceded to the press.

In 1856 he was joined in London by his old friend Nikolay Ogarev. The two worked together on their Russian periodical Kolokol ("Bell"). Soon Herzen began an affair with Ogarev's wife Natalia Tuchkova, daughter of the war hero general Tuchkov. Tuchkova bore Herzen three more children. Ogarev found a new wife and the friendship between Herzen and Ogarev survived.

As the first independent Russian political publisher, Herzen began publishing The Polar Star, a review which appeared infrequently and was later joined by The Bell, a journal issued between 1857 and 1867 at Herzen's personal expense. Both publications acquired great influence via an illegal circulation in Russian territory; it was said the Emperor himself read them. Both publications gave Herzen influence in Russia reporting from a liberal perspective about the incompetence of the Tsar and the Russian bureaucracy.

He was first cousin to Count Sergei Lvovich Levitsky, considered the patriarch of Russian photography and one of Europe's most important early photographic pioneers, inventors and innovators. In 1860, Levitsky would immortalize Herzen in a famous photo capturing the writer's essence and being.

However his hopes of acting as a uniting force were ended by the January Uprising of 1863/1864, when the liberal support for Tsarist revenge against the Poles ended Herzen's link with them; Herzen had pleaded the insurgents' cause. This breach resulted in a declining readership for The Bell, which ceased publication in 1867. By his death in 1870, Herzen was almost forgotten.

In 1864, Herzen returned to Geneva, and after some time went to Paris, where he died in 1870 of tuberculosis complications. Originally buried in Paris, his remains were taken to Nice.

Herzen opposed the aristocracy that ruled 19th century Russia and supported an agrarian collectivist model of social structure. A rise in populism by 1880 led to a favorable re-evaluation of his writings.

Russian Thinkers (The Hogarth Press, 1978), a collection of Berlin's essays in which Herzen features, was the inspiration for Tom Stoppard's The Coast of Utopia, a trilogy of plays performed at London's National Theatre in 2002 and at New York's Lincoln Center in 2006-2007. Set against the background of the early development of Russian socialist thought, the Revolutions of 1848 and later exile, the plays examine the lives and intellectual development of, among other Russians, the anarchist Mikhail Bakunin, the literary critic Vissarion Belinsky, the Novelist Ivan Turgenev and Herzen, whose character dominates the plays.