Following Sher Shah's death and disputed succession, Humayun reconquered Delhi in 1555, leading an army provided by his Persian ally Shah Tahmasb. A few months later, 1556 Humayun died from an accident, soon after regaining his throne. Akbar succeeded his father on February 14, 1556. On November 5, 1556 Akbar's Mughal army defeated forces of General Hemu at the Second battle of Panipat, fifty miles north of Delhi, effectively granting the throne of India to Akbar.

Akbar was only 13 years old when he became emperor. The regency belonged to Bairam Khan, a Turkoman noble. Khan successfully dealt with pretenders to the throne, and improved the discipline of the Mughal armies. These moves helped to consolidate Mughal power in the newly recovered empire. With order somewhat restored, Akbar took the reins of government into his own hands with a proclamation issued in March 1560. (Some historians speculate that Bairam Khan attempted to dethrone or murder Akbar when he came of age; or that Akbar, suspicious of Khan's ambitions and loyalties, encouraged him to perform a pilgrimage to Mecca, and had him killed.)

When Akbar ascended the throne, only a small portion of what had formerly comprised the Mughal empire was still under his control. Akbar devoted himself to the recovery of the remaining provinces, and recognized the importance of the Rajput kingdoms. Rather than attempting to subdue the Rajputs militarily, Akbar decided to pursue diplomacy. He persuaded th Kacchwaha Rajput rulers of Amber(modern day Jaipur) to a matrimonial alliance: The King of Amber's daughter, Hira Kunwari, became Akbar's queen. She took the name Mariam-uz-Zamani was the mother of Prince Salim, who later became the Mughal emperor Jahangir.

The other Rajput kingdoms also married daughters to Akbar, until only two Rajput clans remained against him. The Sisodiyas of Mewar and Hadas (Chauhans) of Ranthambore. Finally Raja Man Singh of Amber went with Akbar to meet the Hada leader, Surjan Hada, to effect an alliance. Surjan grudgingly accepted an alliance — on the condition that Akbar not marry any of his daughters. Surjan later moved his residence to Banaras.

Akbar expanded the Mughal empire to include Malwa (1562), Gujarat (1572), Bengal (1574), Kabul (1581), Kashmir (1586), and Kandesh (1601), among others. Akbar installed a governor over each of the conquered provinces, under his authority.

Akbar did not want to have his court tied too closely to the city of Delhi. He ordered the court moved to Fatehpur Sikri, near Agra, but when this site proved untenable, he set up a roaming camp that let him keep a close eye on what was happening throughout the empire. He tried to develop and encourage commerce. He had the land accurately surveyed for the purpose of correctly evaluating taxation; and he gave strict commands to prevent extortion on the part of the tax gatherers.

Akbar is said to be a benevolent and wise ruler, a man of new ideas, and a sound judge of character. As a ruler, he was able to win the love and reverence of his subjects. Fazal, and even the hostile critic Badayuni, described him as having a commanding personality. He was fearless in the chase as well as in the field of battle, and, "like Alexander of Macedon, was always ready to risk his life, regardless of political consequences". He often plunged his horse into the full-flooded river during the rainy seasons and safely crossed over to the other side. Though a mighty conqueror, he did not usually indulge in cruelty. He is said to be affectionate towards his relatives. He pardoned his brother Hakim, who was a repented rebel. However, on some rare occasions, he dealt cruelly with the offenders, as is shown by his behavior towards his maternal uncle, Muazzam, and his foster-brother, Adam Khan.

He is said to have been extremely moderate in his diet. According to records, he was fond of fruits and had little liking for meat, which he ceased to take altogether in his later years.

Many of the historians are of the opinion that Emperor Akbar possessed inordinate "lust" for women. It is also believed that he was a hard alcoholic as well.... Akbar habitually drank hard. The good father had boldly dared to reprove the emperor sharply for his licentious relations with women. Akbar, instead of resenting the priests audacity, blushingly excused himself.
Even Abul Fazl has highlighted his majesty's love for wine and women. Historians have different opinion on the text mentioned in Ain-i-Akbari. Many refer it as the mention of Emperor's care and affection to protect women, especially virgins. It was his administrative excellence to manage the affairs even though he had permitted wine and prostitution near the palace. His critics do not subscribe to these views, many consider him otherwise.

At the time of Akbar's rule, the Mughal Empire included both Hindus and Muslims. Profound differences separate the Islamic and Hindu faith. When Akbar commenced his rule, a majority of the subjects in the Mughal Empire were Hindus. However, the rulers of the empire were almost exclusively Muslim. In this highly polarized society, Akbar fostered tolerance for all religions. He not only appointed Hindus to high posts, but also tried to remove all distinctions between the Muslims and non-Muslims. He abolished the pilgrim tax in the eighth year and the jizya in the ninth year of his reign, and inaugurated a policy of universal toleration. He also enjoyed a good relationship with the Catholic Church, who routinely sent Jesuit priests to debate, and at least three of his Grandsons were baptized as Catholics (though they did become Muslim later in life).

Akbar built a building called Ibadat Khana (House of Worship), where he encouraged religious debate. Originally, this debating house was open only to Sunnis, but following a series of petty squabbles which turned ugly Akbar encouraged Hindus, Catholics and even atheists to participate. He tried to reconcile the differences of both religions by creating a new faith called the Din-i-Ilahi ("Faith of the Divine"), which incorporated both Islam and Hinduism, and even some elements of Christianity and Jainism. This faith, however, was not for the masses. In fact, the only "converts" to this new religion were the upper nobility of Akbar's court. Historians have so far been able to identify only 18 members of this new religion. He also married several Hindu princesses, though many consider that to be politically motivated rather than a genuine attempt at religious reconciliation.

His moves from Islam, while welcomed by the Hindu majority, where not appreciated by the Muslim faithful. Rumours were rife that Mosques were being closed and destroyed, that those who entered his Harem were required to say "There is no God but Allah, and Akbar is his messenger" a bastardised version of the traditional Muslim Shahada, or declaration of faith. When Akbar opened a wine shop, it was believed he also ordered pigs blood to be mixed with the mixture. Many members of the ulema began to protest his actions, and Ahmad Sarhindi (Who had been nick-named "Mujaddid" or "Renovator" [of islam]) wrote tracts rejecting the Shirk that he believed Akbar was guilty of. He was to be arrested by Jahangir upon his successon. Ultimately, despite Akbars attempts at reconciling the two major faiths, by the end of the 16th Century community relations were to be worse than when Akbar ascended to power.

Although Akbar was illiterate, he had a fine literary taste. He took interest in philosophy, theology, history, and politics. He maintained a library full of books on various subjects, and was fond of the society of scholars, poets and philosophers, who read books to him aloud, and thus enabled him to be conversant with Sufi, Christian, Zoroastrian, Hindu and Jain literature. He used to invite scholars from different religions for discussions with him. Smith wrote that "anybody who heard him arguing with acuteness and lucidity on a subject of debate would have credited him with wide literary knowledge and profound erudition and never would have suspected him of illiteracy". He was a patron to many literary figures, including the brothers Feizi and Abul-Fazel. The former was commissioned by Akbar to translate a number of Sanskrit scientific works into Persian; and the latter produced the Akbarnama, an enduring record of the emperor's reign. It is also said that Akbar employed Jerome Xavier (nephew of Francis Xavier) , a Jesuit missionary, to translate the four Gospels of the New Testament into Persian.

Akbar also possessed a fair taste of art, architecture and mechanical works, and is credited with many inventions and improvements in the manufacture of matchlocks. He erected a vast administrative machinery on a comprehensive plan, He looked, as we know from the Ain-i-Akbari, "upon the smallest details as mirror capable of reflecting a comprehensive outline.

The last few years of Akbar's reign were troubled by the misconduct of his sons. Two of them died in their youth, the victims of intemperance. The third, Salim, later known as Emperor Jahangir, was frequently in rebellion against his father. Asirgarh, a fort in the Deccan, proved to be the last conquest of Akbar, taken in 1599 as he proceeded north to face his son's rebellion. Reportedly, Akbar keenly felt these calamities, and they may even have affected his health and hastened his death, which occurred in Agra. His body was interned in a magnificent mausoleum at Sikandra, near Agra.