In 1583, when Mehmed was appointed the sancak-bey of Saruhan, Handan being beautiful was presented to him at his departure by Mehmed Pasha and Gevherhan Sultan. When Mehmed ascended the throne after his father's death in 1595, Handan came to Istanbul with him.
When Ahmed ascended the throne following Mehmed III's death on 22 December 1603, Handan became Valide Sultan. As the mother of the new Sultan, she received 1,000 aspers a day. On Friday 9 January, the former Valide Sultan Safiye Sultan, along with Şehzade Mustafa, were sent to live in the Eski Palace located at the Beyazıt Square. Soon after his succession, Ahmed wanted to express his gratitude to Mehmed Pasha and Gevherhan Sultan for the role they had played in bringing his parents together. By then, however, Cerrah Mehmed Pasha was old and ailing, and died on 9 January 1604. Ahmed, therefore, honored the late pasha's wife. He also named one of his daughters after her.
As regent
As a co-regent, she immediately began building up her network of clients, and was actively involved in the running of dynastic and imperial affairs together with Ahmed's tutor Mustafa Efendi. Ahmed several times announced his eagerness to go to war. It seems that Handan Sultan and Mustafa Efendi advised him to behave in this manner in order to give the public the impression that he was capable of ruling the state. He also began to spend a great deal of time outside the palace, notably hunting or conducting incognito inspections, regardless of the weather. Handan Sultan quickly realized that her son could easily put himself in danger and thus needed to be closely watched. She favored her fellow Bosnians at her son's court. She convinced Ahmed to appoint Yavuz Ali Pasha as grand vizier, and maintained a close relationship with him, especially during the first critical months of Ahmed's reign. In spring of 1604, she and Mustafa Efendi ordered Ali Pasha to take command in Hungary. In August 1604, Ahmed ordered the execution of deputy grand vizier Kasim Pasha, and in January 1605 of his successor Sarıkçı Mustafa Pasha, and in both cases his decision was approved and encouraged by Handan Sultan and Mustafa Efendi, who were trying to rid the court of clients of Safiye Sultan. Because of Handan Sultan's influence on her son, Dervish Mehmed Agha replaced Bayran Agha as chief gardener in summer of 1604. Whenever Handan, Ahmed, and Derviş got altogether in the palace gardens, she made Ahmed promise that he will not do anything contrary to Derviş's words and thoughts. Thanks to Handan's continuous support, he managed to become the first royal favorite of Ahmed. Handan Sultan also acted as an intermediary between her son and other government officials. Any vizier who wanted to communicate with Ahmed had to submit his petition first to her. The contemporary historian Ibrahim Peçevi questioned her wisdom, but legitimized her authority over her son by an old and popular saying "a mother's right is God's right".
Charities
Handan Sultan made an endowment for the maintenance of her husband Mehmed III's tomb and the salaries of its employees. She also made endowments in Kütahya, Menemen and Kilizman.
Illness
Sinanpaşaoğlu Mehmed Pasha who had been married to Piyale Pasha and Gevherhan Sultan's daughter in November 1598, was sent to quell the Jelali rebellions in Anatolia. However, he proved to be ineffective, and conducted himself so inappropriately as to arouse suspicions that he had turned a rebel himself. With Handan's intervention, he was forgiven by the sultan. He returned to Istanbul, and took up his duties as vezir. However, he was executed on 20 August 1605. Handan, who was already ill at that time, was so shocked by the turn of events that her condition reportedly worsened.
Death and aftermath
Handan Sultan died at the Topkapı Palace on Wednesday, 9 November 1605 after a long illness. At her funeral, large amounts of food and alms were distributed for the sake of her soul. She was buried next to her husband in his mausoleum in Hagia Sophia Mosque, Istanbul. Ahmed despite appeals of the viziers for the customary mourning for seven days, didn't postpone his departure from Istanbul on campaign against the Jelali revolts. After Handan's death, Haci Mustafa Agha, the chief eunuch of the imperial harem throughout Ahmed's reign, became the highest authority in the harem.