At the age of nine, Ruqaiya married

At the age of nine, Ruqaiya married her first cousin, Akbar, in November of 1551 at Kabul, Afghanistan, shortly after his first appointment as a Viceroy in the province of Ghazni.[10] The marriage was arranged by Ruqaiya's uncle and Akbar's father, Humayun, and took place soon after the untimely death of Ruqaiya's father, Hindal Mirza, who died in a battle.[11] Humayun conferred on the young couple, all the wealth, army and adherents of his deceased younger brother, Hindal, and Ghazni, which was one of Hindal's jagir, was given to his nephew and son-in-law, Akbar.[11][12]

Ruqaiya became an Empress of the Mughal Empire at the age of fourteen years following her husband's accession to the throne in 1556.

Throughout her 53 years of marriage, Ruqaiya remained childless, but was given the primary responsibility for the upbringing of her grandson, prince Khurram (the future Emperor Shah Jahan).[13]

Just prior to Khurram’s birth, a soothsayer had reportedly predicted to Ruqaiya Sultan Begum that the still unborn child was destined for imperial greatness. So, when Khurram was born in 1592 and was only six days old, Akbar ordered that the prince be taken away from his mother and handed him over to Ruqaiya so that he could grow up under her care and Akbar could fulfill his aging wife's wish, to raise a Mughal emperor.[7] Khurram remained with her,[3] until he had turned 13. The young prince was then, finally, allowed to return to his father's household, and thus, be closer to his biological mother.[7] Ruqaiya oversaw Khurram's education as well for she, unlike her husband, was well educated.[14] Ruqaiya and Khurram, therefore, shared a close relationship much like the relationship that Akbar had shared with Khurram (the prince had been a favourite of his grandfather). Khurram's father and Ruqaiya's step-son, Jahangir, noted that Ruqaiya had loved Khurram "a thousand times more than if he had been her own son".[3]

Despite the fact that she did not bear him any children, she was always kept in high regard by her husband, as he held great respect and affection for her. Ruqaiya was thus, a senior and high ranked figure in the imperial harem, along with the other two chief Empresses, also and at court during her husband's reign as well as in his successor's (Jahangir) reign.[15] She took a precedence over other wives of Akbar in terms of birth. She was his only wife who was the most supreme in terms of birth, being herself a Timurid princess and thus, a member of the Timurid dynasty.

The Empress also took active part in court politics just like Salima sultan begum and Mariam-uz-Zamani. In the early 1600s, Ruqaiya, Salima Sultan Begum and Maryam Makani, along with other ladies of the harem, played a crucial role in negotiating a settlement between Akbar and Jahangir, (when their relationship had turned sour), eventually helping to pave the way for Jahangir's accession to the throne.[7][16] During Jahangir's reign, Ruqaiya and Salima Sultan Begum again played a crucial role in successfully securing pardon for the powerful, Khan-i-Azam, Mirza Aziz Koka, who had been sentenced to death by Jahangir. Apart from her own palace at Fatehpur Sikri, Ruqaiya owned palaces outside the fort in Agra, near the Jamuna river, a privilege given to Mughal princesses only and sometimes to empresses who were kept in high esteem.[17][18]

In 1607, Ruqaiya went for a pilgrimage to the mausoleum of her father Hindal, in Kabul, while being accompanied by both Jahangir and Khurram. Within the same year, Sher Afghan Quli Khan, the jagirdar of Burdwan died and his widowed wife, Mehrunnissa (later Empress Nur Jahan) was summoned to Agra by Jahangir to act as lady-in-waiting to the Empress Ruqaiya.[10] Given the precarious political connections of Sher Afghan before his death, his family was in great danger and therefore for her own protection, Mihrunnissa needed to be at the court in Agra.

Nur Jehan and her daughter, Ladli Begum, served as ladies-in-waiting to the Empress for four years while earnestly endeavouring to please their imperial mistress.[19] The relationship that grew up between Ruqaiya and Mihrunnissa appears to have been an extremely tender one which remained so until Ruqaiya's death in 1626. The Dutch merchant, Pieter van den Broecke said: "This Begum [Ruqaiya] conceived a great affection for Mehr-un-Nissa; she loved her more than others and always kept her in her company