It was during Alexander II's rule that the Caucasian War (1817–1864) reached its climax. Just before the conclusion of the war with a victory on Russia's side, the Russian Army, under the emperor's order, sought to eliminate the Circassian "mountaineers" in what would be often referred to as "cleansing" in several historic dialogues.

In the period of his life as heir apparent (1825 to 1855), the intellectual atmosphere of Saint Petersburg did not favour any kind of change: freedom of thought and all forms of private initiative were suppressed vigorously by the order of his father. Personal and official censorship was rife; criticism of the authorities was regarded as a serious offence.

In 1838–39, as a young bachelor, Alexander made the Grand Tour of Europe which was standard for young men of his class at that time. One of the purposes of the tour was to select a suitable bride for himself. He stayed for three days with the maiden Queen Victoria, who was already Queen although she was one year younger than him. The two got along well, but there was no question of marriage between two major monarchs. Alexander went on to Germany, and in Darmstadt, he met and was charmed by the 15-year-old daughter of Louis II, Grand Duke of Hesse. On 16 April 1841, aged 23, Tsarevitch Alexander married Princess Marie of Hesse in St. Petersburg, The bride had previously been received into the Russian Orthodox Church and had taken a new name; she would thereafter be known as Maria Alexandrovna.

The education of the Tsesarevich as Future Emperor took place under the supervision of the liberal romantic poet and gifted translator Vasily Zhukovsky, grasping a smattering of a great many subjects and becoming familiar with the chief modern European languages. Alexander's alleged lack of interest in military affairs (as detected by later historians) resulted from his reaction to the effects of the unsavoury Crimean War of 1853-1856 on his own family and on the whole country. Unusually for the time, the young Alexander was taken on a six-month tour of Russia (1837), visiting 20 provinces in the country. He also visited many prominent Western European countries in 1838 and 1839. As Tsesarevich, Alexander became the first Romanov heir to visit Siberia (1837).

After Alexander became Emperor in 1855, he maintained a generally liberal course. Despite this, he was a target for numerous assassination attempts (1866, 1879, 1880). On 13 March [O.S. 1 March] 1881, members of the Narodnaya Volya (People's Will) party killed him with a bomb. The Emperor had earlier in the day signed the Loris-Melikov constitution, which would have created two legislative commissions made up of indirectly elected representatives, had it not been repealed by his reactionary successor Alexander III.

In 1856, at the beginning of his reign, Alexander had made a memorable speech to the deputies of the Polish nobility who inhabited Congress Poland, Western Ukraine, Lithuania, Livonia and Belarus, in which he admonished, "Gentlemen, let us have no dreams!" The result was the January Uprising of 1863–1864 that was suppressed after eighteen months of fighting. Hundreds of Poles were executed, and thousands were deported to Siberia. The price for suppression was Russian support for the unification of Germany. Years later, Germany and Russia became enemies.

The emancipation was not merely a humanitarian question capable of being solved instantaneously by imperial ukase. It contained very complicated problems, deeply affecting the economic, social and political Future of the nation. Alexander had to choose between the different measures recommended to him and decide if the serfs would become agricultural laborers dependent economically and administratively on the landlords or if the serfs would be transformed into a class of independent communal proprietors. The Emperor gave his support to the latter project, and the Russian peasantry became one of the last groups of peasants in Europe to shake off serfdom. The Architects of the emancipation manifesto were Alexander's brother Konstantin, Yakov Rostovtsev, and Nikolay Milyutin. On 3 March 1861, six years after his accession, the emancipation law was signed and published.

In 1863, Alexander II re-convened the Diet of Finland and initiated several reforms increasing Finland's autonomy within the Russian Empire, including establishment of its own currency, the markka. Liberation of Business led to increased foreign investment and industrial development. Finland also got its first railways, separately established under Finnish administration.

By his Empress consort, Tsarina Maria Alexandrovna, Alexander II had eight children, seven of whom survived into adulthood. He particularly placed hope in his eldest son, Tsarevich Nicholas. In 1864, Alexander II found Nicholas a bride, Princess Dagmar of Denmark, second daughter of King Christian IX of Denmark and younger sister to Alexandra, Princess of Wales and King George I of Greece. However, in 1865, during the engagement, Nicholas died and the tsar's second son, Grand Duke Alexander, not only inherited his brother's position of tsarevich, but also his fiancée. The couple married in November 1866, with Dagmar converting to Orthodoxy and taking the name Maria Feodorovna.

At home, Tsarina Marie Alexandrovna was suffering from tuberculosis and was spending increasing time abroad. In 1866, Alexander II took a mistress, Princess Catherine Dolgorukya, with whom he would father three surviving children. The affair, in the face of the tsarina's declining health, served to alienate the rest of his adult children, save his son Alexei and his daughter, who, like Alexander II's brothers, believed that the tsar was beyond criticism. In 1880, however, following threats on Catherine's life, the tsar moved his mistress and their children into the Winter Palace, installing them in rooms directly above the apartments of his ailing wife. When Grand Duchess Marie Alexandrovna made a visit in May 1880, being warned that her mother was dying, she was horrified to learn of his father's mistress' living arrangements and confronted her father. Shocked by the loss of support from his daughter, he quietly retreated to Gatchina Palace for military reviews. The quarrel, however, evidently, jolted his conscience enough to lead him to return to St. Petersburg each morning to ask after his wife's health. The tsarina, however, had not much longer to live, dying on 3 June [O.S. 22 May] 1880. On 18 July [O.S. 6 July] 1880, Alexander II and Catherine were married in a secret ceremony at Tsarskoe Selo. The action scandalized both his family and the court, also violating Orthodox custom which required a minimum period of 40 days mourning between the death of a spouse and the remarriage of a surviving spouse, eliciting criticism in foreign courts. Alexander also bestowed on Catherine the title of Princess Yurievskaya and legitimized their children.

During the 1867 World Fair Polish immigrant Antoni Berezowski attacked the carriage with Alexander, his two sons and Napoleon III. His self-modified, double-barreled pistol misfired and only a horse of an escorting cavalryman was hit.

In time, political differences, and other disagreements, led to estrangement between the two Alexanders. Amongst his children, he remained particularly close with his second, and only surviving daughter, Grand Duchess Marie Alexandrovna. In 1873, a quarrel broke out between the courts of Queen Victoria and Alexander II, when Victoria's second son, Prince Alfred, made it known that he wished to marry the Grand Duchess. The tsar objected to the queen's request to have his daughter come to England in order to meet her, and after the January 1874 wedding in St. Petersburg, the tsar insisted that his daughter be granted precedence over the Princess of Wales, which the queen rebuffed. Later that year, after attending the engagement ceremonies of his second surviving son, Vladimir, to Marie of Mecklenburg-Schwerin in Berlin, Alexander II, with his third son, Alexei, accompanying him, made a visit to England. While not a state visit, but simply a trip to see his daughter, he nevertheless partook in receptions at Buckingham Palace and Marlborough House, inspected the artillery at the Royal Arsenal in Woolwich, reviewed troops at Aldershot and met both Prime Minister Benjamin Disraeli and leader of the opposition, william Gladstone. Disraeli observed of the tsar that "his mien and manners are gracious and graceful, but the expression of his countenance, which I could now very closely examine, is sad. Whether it is satiety, or the loneliness of despotism, or fear of a violent death, I know not, but it was a visage of, I should think, habitual mournfulness."

In response to the overwhelming defeat (1856) suffered by Russia in the Crimean War and to attempt to keep pace with military advances in other European countries, Alexander II appointed Dmitry Milyutin to carry out significant reforms in the Russian armed forces. The changes included universal military conscription, introduced for all social classes on 1 January 1874. Prior to this new regulation, as of 1861, conscription was compulsorily enforced only for the peasantry. Conscription had, prior to this reform, been 25 years for serfs that were drafted by their landowners, which was widely considered to be a life sentence. Other military reforms included extending the reserve forces and the military district system, which split the Russian states into 15 military districts, a system still in use over a hundred years later. The building of strategic railways and an emphasis on the military education of the officer corps comprised further reforms. Corporal punishment in the military and branding of Soldiers as punishment were banned. The bulk of important military reforms were enacted as a result of the poor showing in the Crimean War.

Alexander II appears prominently in the opening two chapters of Jules Verne's Michael Strogoff (published in 1876 during Alexander's own lifetime). The Emperor sets the book's plot in motion and sends its eponymous protagonist on the dangerous and vital mission which would occupy the rest of the book. Verne presents Alexander II in a highly positive light, as an enlightened yet firm monarch, dealing confidently and decisively with a rebellion. Alexander's liberalism shows in a dialogue with the chief of police, who says "There was a time, sire, when NONE returned from Siberia", to be immediately rebuked by the Emperor who answers: "Well, whilst I live, Siberia is and shall be a country whence men CAN return."

The Russian Emperor was successful in his diplomatic endeavours. Having secured agreement to non-involvement by the other Great Powers, on 17 April 1877 Russia declared war upon the Ottoman Empire. The Russians were successful against the Turks and the Russo-Turkish War of 1877–1878 ended with the signing of the preliminary peace Treaty of San Stefano on 19 February (3 March N.S.) 1878. The treaty and the subsequent Congress of Berlin secured the emergence of an independent Bulgarian state for the first time since 1396, and the tsar's nephew, Prince Alexander of Battenberg, was elected as the Bulgarians' first ruler. For his social reforms in Russia and his role in the liberation of Bulgaria, Alexander II became known in Bulgaria as the "Tsar-Liberator of Russians and Bulgarians". A monument to Alexander II was erected in 1907 in Sofia in the "National Assembly" square, opposite to the Parliament building. The monument underwent a complete reconstruction in 2012, funded by the Sofia Municipality and some Russian foundations. The inscription on the monument reads in Old-Bulgarian style: "To the Tsar-Liberator from grateful Bulgaria". There is a museum dedicated to Alexander in the Bulgarian city of Pleven.

The student acted on his own, but other Revolutionaries were keen to murder Alexander. In December 1879, the Narodnaya Volya (People's Will), a radical revolutionary group which hoped to ignite a social revolution, organised an explosion on the railway from Livadia to Moscow, but they missed the emperor's train.

Oscar Wilde's first play Vera; or, The Nihilists, written in 1880—Alexander II's last year—features Russian Revolutionaries who seek to assassinate a reform-minded Emperor (and who, in the play, ultimately fail in their plot). Though Wilde's fictional Emperor differs from the actual Alexander, contemporary events in Russia – as published in the British press of the time – clearly influenced Wilde.

On 13 March [O.S. 1 March] 1881, Alexander fell victim to an assassination plot in Saint Petersburg.

With construction starting in 1883, the Church of the Savior on Blood was built on the site of Alexander's assassination and dedicated in his memory.

The films Katia (1938) and Magnificent Sinner (1959) depict a highly fictionalized account of the Tsar's romance with the woman who became his second wife.

In The Tiger in the Well, Philip Pullman refers to the assassination – though he never names Alexander – and to the pogroms that followed. The anti-Jewish attacks play an important role in the novel's plot. Andrew Williams's historical thriller, To Kill A Tsar, tells the story of The People's Will Revolutionaries and the assassination through the eyes of an Anglo-Russian Doctor living in St Petersburg.

Finally, the tsar's assassination also inspired anarchists to advocate "'propaganda by deed'—the use of a spectacular act of violence to incite revolution."