During the Revolutions of 1848 the Austrian Chancellor Prince Metternich resigned (March–April 1848). The young Archduke, who (it was widely expected) would soon succeed his uncle on the throne, was appointed Governor of Bohemia on 6 April 1848, but never took up the post. Sent instead to the front in Italy, he joined Field Marshal Radetzky on campaign on 29 April, receiving his baptism of fire on 5 May at Santa Lucia.

On 7 December 1848, the Diet of Hungary formally refused to acknowledge the title of the new king, “as without the knowledge and consent of the diet no one could sit on the Hungarian throne” and called the nation to arms. From a legal point of view, according to the coronation oath, a crowned Hungarian King can not reliquish from the Hungarian throne during his life, if the king is alive and unable do his duty as ruler, a governor (or regent with proper English terminology) had to deputize the royal duties. Constitutionally, his uncle, Ferdinand remained still the legal king of Hungary. If there is no possibility to inherit the throne automatically due to the death of the predecessor king (as king Ferdinand was still alive), but the monarch wants to reliquish his throne and appoint an other king before his death, technically only one legal solution has remained: the parliament had the power to dethronize the king and elect his successor as the new king of Hungary. Due to the legal and military tensions, the Hungarian parliament did not make that favor for Franz Joseph. This event gave to the revolt an excuse of legality. Actually, from this time until the collapse of the revolution, Lajos Kossuth (as elected regent-president) became the de facto and de jure ruler of Hungary.

Following the accession of Franz Joseph to the throne in 1848, the political representatives of the Kingdom of Bohemia hoped and insisted that account should be taken of their historical state rights in the upcoming constitution. They felt the position of Bohemia within the Habsburg Monarchy should have been highlighted by a coronation of the new ruler to the king of Bohemia in Prague (the last coronation took place in 1836). However before the 19th century the Habsburgs had ruled Bohemia by hereditary right and a separate coronation was not deemed necessary.

In contrast to his predecessor Emperor Ferdinand (who spent the rest of his life after his abdication in 1848 in Bohemia and especially in Prague), Franz Joseph was never crowned separately as king of Bohemia. In 1861, the negotiations failed because of unsolved constitutional problems. However in 1866, a visit of the monarch to Prague following the defeat at Hradec Králové (Königgrätz) was a huge success, testified by the considerable numbers of new photographs taken.

Under the guidance of the new prime minister Prince Schwarzenberg the Third, the new emperor at first pursued a cautious course, granting a constitution in early 1849. At the same time, a military campaign was necessary against the Hungarians, who had rebelled against Habsburg central authority in the name of their ancient constitution. Franz Joseph was also almost immediately faced with a renewal of the fighting in Italy, with King Charles Albert of Sardinia taking advantage of setbacks in Hungary to resume the war in March 1849.

The Hungarian reform laws (April laws) were based on the 12 points that established the fundaments of modern civil and political rights, economic and societal reforms in Kingdom of Hungary. The crucial turning point of the Hungarian events were the April laws which was ratified by his uncle King Ferdinand, however the new young Austrian monarch Francis Joseph arbitrarily “revoked” the laws without any legal competence. The monarchs had no right to revoke Hungarian parliamentary laws which were already signed. This unconstitutional act irreversibly escalated the conflict between the Hungarian parliament and Francis Joseph. The Austrian Stadion Constitution was accepted by the Imperial Diet of Austria, where Hungary had no representation, and which traditionally had no legislative power in the territory of Kingdom of Hungary; despite of this, it also tried to abolish the Diet of Hungary (which existed as the supreme legislative power in Hungary since the late 12th century.) The new Austrian constitution also went against the historical constitution of Hungary, and even tried to nullify it. These events represented a clear and obvious existential threat for the Hungarian state. The new constrained Stadion Constitution of Austria, the revoke of the April laws and the Austrian military campaign against Kingdom of Hungary resulted in the fall of the pacifist Batthyány government (which sought agreement with the court) and led to the sudden emergence of Lajos Kossuth’s followers in the Hungarian parliament, who demanded the full independence of Hungary. On 7 March 1849 an imperial proclamation was issued in the name of the emperor Francis Joseph, according to the new proclamation, the territory of Kingdom of Hungary would be administered by five military districts, while Principality of Transylvania would be reestablished. The Austrian military intervention in the Kingdom of Hungary resulted in strong anti-Habsburg sentiment among Hungarians, thus the events in Hungary grew into a war for total independence from the Habsburg dynasty.

In addition, he founded the Order of Franz Joseph (Franz Joseph-Orden) on 2 December 1849, and the Order of Elizabeth (Elizabeth-Orden) in 1898.

The next few years saw the seeming recovery of Austria’s position on the international scene following the near disasters of 1848–1849. Under Schwarzenberg’s guidance, Austria was able to stymie Prussian scheming to create a new German Federation under Prussian leadership, excluding Austria. After Schwarzenberg’s premature death in 1852, he could not be replaced by statesmen of equal stature, and the Emperor himself effectively took over as prime minister.

On 18 February 1853, Franz Joseph survived an assassination attempt by Hungarian nationalist János Libényi. The emperor was taking a stroll with one of his officers, Count Maximilian Karl Lamoral O’Donnell, on a city bastion, when Libényi approached him. He immediately struck the emperor from behind with a knife straight at the neck. Franz Joseph almost always wore a uniform, which had a high collar that almost completely enclosed the neck. The collars of uniforms at that time were made from very sturdy material, precisely to counter this kind of attack. Even though the Emperor was wounded and bleeding, the collar saved his life. Count O’Donnell struck Libényi down with his sabre.

However, Franz Joseph fell deeply in love with Néné’s younger sister Elisabeth (“Sisi”), a beautiful girl of fifteen, and insisted on marrying her instead. Sophie acquiesced, despite her misgivings about Sisi’s appropriateness as an imperial consort, and the young couple were married on 24 April 1854 in St. Augustine’s Church, Vienna.

His new government installed the system of neoabsolutism in Austrian internal affairs to make the Austrian Empire a unitary, centralised and bureaucratically administered state. When Franz Joseph returned to constitutional rule after the debacles in Italy at Magenta and Solferino and summoned the diets of his lands, the question of his coronation as king of Bohemia again returned to the agenda, as it had not since 1848. On 14 April 1861, Emperor Franz Joseph received a delegation from the Bohemian Diet with his words (in Czech):

In 1867, the Austro-Hungarian compromise and the introduction of the dual monarchy left the Czechs and their aristocracy without the recognition of separate Bohemian state rights for which they had hoped. Bohemia remained Austrian Crown Lands. In Bohemia, opposition to dualism took the form of isolated street demonstrations, resolutions from district representations, and even open air mass protest meetings, confined to the biggest cities, such as Prague. The Czech newspaper Národní listy, complained that the Czechs had not yet been compensated for their wartime losses and sufferings during the Austro-Prussian War, and had just seen their historic state rights tossed aside and their land subsumed into the “other” half of the Austro-Hungarian Monarchy, commonly called “Cisleithania”.

The Czech hopes were revived again in 1870–1871. In an Imperial Rescript of 26 September 1870, Franz Joseph referred again to the prestige and glory of the Bohemian Crown and to his intention to hold a coronation. Under Minister-President Karl Hohenwart in 1871, the government of Cisleithania negotiated a series of fundamental articles spelling out the relationship of the Bohemian Crown to the rest of the Habsburg Monarchy. On 12 September 1871, Franz Joseph announced:

Franz Joseph founded in 1872 the Franz Joseph University (Hungarian: Ferenc József Tudományegyetem, Romanian: Universitatea Francisc Iosif) in the city of Cluj-Napoca (at that time a part of Austria-Hungary under the name of Kolozsvár). The university was moved to Szeged after Cluj became a part of Romania, becoming the University of Szeged.

In 1873, two years after the unification of Germany, Franz Joseph entered into the League of Three Emperors (Dreikaiserbund) with Kaiser Wilhelm I of Germany and Tsar Alexander II of Russia, who was succeeded by Tsar Alexander III in 1881. The league had been designed by the German chancellor Otto von Bismarck, as an attempt to maintain the peace of Europe. It would last intermittently until 1887.

Franz Joseph Land in the Russian Arctic was named in his honour in 1873 by the Austro-Hungarian North Pole expedition which first reported finding it. The Franz Joseph Glacier in New Zealand’s South Island also bears his name.

In 1885 Franz Joseph met Katharina Schratt, a leading actress of the Vienna stage, and she became his friend and confidante. This relationship lasted the rest of his life, and was—to a certain degree—tolerated by Elisabeth. Franz Joseph built Villa Schratt in Bad Ischl for her, and also provided her with a small palace in Vienna. Though their relationship lasted for thirty-four years, it remained platonic.

Their marriage would eventually prove to be an unhappy one; though Franz Joseph was passionately in love with his wife, the feeling was not mutual. Elisabeth never truly acclimatized to life at court, and was frequently in conflict with the imperial family. Their first daughter Sophie died as an infant, and their only son Rudolf died by suicide in 1889 in the infamous Mayerling Incident.

Archduke Franz Ferdinand became heir presumptive (Thronfolger) to the throne of Austria-Hungary in 1896, after the deaths of his cousin Rudolf (in 1889) and his father Karl Ludwig (in 1896). The relationship between him and Franz Joseph had always been a fairly contentious one, which was further exacerbated when Franz Ferdinand announced his desire to marry Countess Sophie Chotek, a match that was out of the question in the mind of the emperor, as Sophie was merely of nobility as opposed to being of dynastic rank.

The Empress was an inveterate traveller, horsewoman, and fashion maven who was rarely seen in Vienna. Sisi was obsessed about preserving her beauty, carrying out many bizarre routines and strenuous exercise, and as a result suffered from ill health. She was stabbed to death by an Italian anarchist in 1898 while on a visit to Geneva. A few days after the funeral, Robert of Parma wrote in a letter to his friend Tirso de Olazábal that “It was pitiful to look at the Emperor, he showed a great deal of energy in his immense pain, but at times one could see all the immensity of his grief.” Franz Joseph never fully recovered from the loss. According to the future empress Zita of Bourbon-Parma he told his relatives: “You’ll never know how important she was to me” or, according to some sources, “You will never know how much I loved this woman.”

Although the emperor received letters from members of the imperial family throughout the fall and winter of 1899 beseeching him to relent, Franz Joseph stood his ground. He finally gave his consent in 1900; however, the marriage was to be morganatic, and any children of the marriage would be ineligible to succeed to the throne. The couple were married on 1 July 1900 at Reichstadt. The emperor did not attend the wedding, nor did any of the archdukes. After that, the two men disliked and mistrusted each other.

In 1903, Franz Joseph’s veto of Cardinal Mariano Rampolla’s election to the papacy was transmitted to the Papal conclave by Cardinal Jan Puzyna de Kosielsko. It was the last use of such a veto, as the new Pope Pius X prohibited future uses and provided for excommunication for any attempt.

Franz Joseph’s German identity was made explicitly clear during a meeting in August 1908 between himself and Edward VII when the latter tried to persuade him to abandon Austria-Hungary’s alliance with Germany for co-operation with Britain; Franz Joseph replied that he was a “loyal ally” and said “I am a German prince.”

In 1908, the Russian foreign minister, Alexander Izvolsky, offered Russian support, for the third time, for the annexation of Bosnia and Herzegovina by Austria-Hungary, in exchange for Austrian support for the opening of the Bosporus Strait and the Dardanelles to Russian warships. Austria’s foreign minister, Alois von Aehrenthal, pursued this offer vigorously, resulting in the quid pro quo understanding with Izvolsky, reached on 16 September 1908 at the Buchlau Conference. However, Izvolsky made this agreement with Aehrenthal without the knowledge of Tsar Nicholas II or his government in St. Petersburg, or any of the other foreign powers including Britain, France and Serbia.

Based upon the assurances of the Buchlau Conference and the treaties that preceded it, Franz Joseph signed the proclamation announcing the annexation of Bosnia-Herzegovina into the Empire on 6 October 1908. However a diplomatic crisis erupted, as both the Serbs and the Italians demanded compensation for the annexation, which the Austro-Hungarian government refused to entertain. The incident was not resolved until the revision of the Treaty of Berlin in April 1909, exacerbating tensions between Austria-Hungary and the Serbs.

Many Czech people were waiting for political changes in monarchy, including Tomáš Garrigue Masaryk and others. Masaryk served in the Reichsrat (Upper House) from 1891 to 1893 in the Young Czech Party and again from 1907 to 1914 in the Realist Party (which he had founded in 1900), but he did not campaign for the independence of Czechs and Slovaks from Austria-Hungary. In Vienna in 1909 he helped Hinko Hinković’s defense in the fabricated trial against prominent Croats and Serbs members of the Serbo-Croatian Coalition (such as Frano Supilo and Svetozar Pribićević), and others, who were sentenced to more than 150 years and a number of death penalties. The Bohemian question would remain unresolved for the entirety of Franz Joseph’s reign.

On 28 June 1914 Franz Joseph’s nephew and heir Archduke Franz Ferdinand, and his morganatic wife Sophie, Duchess of Hohenberg, were assassinated by Gavrilo Princip, a Yugoslav nationalist of Serbian ethnicity, during a visit to Sarajevo. When he heard the news of the assassination, Franz Joseph said that “one has not to defy the Almighty. In this manner a superior power has restored that order which I unfortunately was unable to maintain.”

Following the assassination of Franz Ferdinand and Sophie in 1914, Franz Joseph’s daughter, Marie Valerie, noted that her father expressed his greater confidence in the new heir presumptive: his grandnephew Archduke Charles. The emperor admitted to his daughter, regarding the assassination: “For me, it is a relief from a great worry.”

Franz Joseph died in the Schönbrunn Palace on the evening of 21 November 1916, at the age of 86. His death was a result of developing pneumonia of the right lung several days after catching a cold while walking in Schönbrunn Park with the King of Bavaria. He was succeeded by his grandnephew Charles I, who reigned until the collapse of the Empire following its defeat in 1918.