Ekber Shah who ascended the throne at the age of fourteen reigned the state for a period of 49 years. Bayram Han who was his chief assistant and his tutor was the competent authority until he came to the age of twenty. Then, he forcibly pensioned him off and sent to Haj. Afterwards, he became the only ruler of the country. He established a powerful organisation. He prevented the rebellions and disintegration. He established dominion entirely in Bengal in the year of 1578, in Kabul in the year of 1581, in Kashmir in the year of 1587, in Sindhi in the year of 1592 and in Kandehar in the year of 1594.

In the period of Ekber Shah, the Indian influence started to increase in the palace. Through the influence and tolerance of the Indian women that were in his harem, he provided the consideration of the Indians as the citizens and the assignation of them as soldiers and state officials. When the equality between the Muslims and the armies was established, the tension diminished. He adopted the approach of "the state for the public, not the public for the state" and he had it approved by the others. Turks constituted a small minority in India with a great population and they generally became soldiers and officials. Since the equality among the people was established in respect of various issues, the domination of the minority over the majority was not a problem any longer.

Ekber Shah became ill in the year of 1603 and he even could not speak due to his illness. He invited his son, Cihangir and he made him put on sword with his own hands and then, he made him wear the turban of sovereignty. Before his death, a construction was started in Sikanda for his mausoleum. However, this mausoleum that reminded of a storey of a pyramid was completed by his son, Cihangir and he was buried there. Ekber Shah had died in the year of 1605.