During his father's reign as ruler of the cities of Yarkand, Kashgar and Khotan, Jahangir did not play a major role in the government. The only event recorded of him during this time is his marriage to Khadija Sultan Khanim, the youngest daughter of Ahmad Khan.
Mirza Aba Bakr's reign was brought to an end in 1514 when Sultan Said Khan invaded Kashgaria. Judging his army to be incapable of putting up an effective resistance, he handed over Yarkand to Jahangir Mirza and promptly headed south for Khotan. Jahangir Mirza, however, having been suddenly thrust into his position with little experience to aid him, decided that maintaining his position in the face of Sultan Said Khan's army would be impossible. Five days after the departure of his father, he destroyed his treasures and allowed the citizens of Yarkand to pillage what they pleased so that it wouldn't fall into the hands of the khan. He then fled south and took refuge in the frontier regions near Ladakh.
Jahangir Mirza was eventually enticed to surrender to Sultan Said Khan. Upon being brought before him he was given a pardon. That winter, however, he was murdered in Yangi Hisar. The identity and motives of the assassins were unknown.
- Muhammad Haidar says (p. 329) that he is 42 years old in 1514, but he is notoriously unreliable with dates.
- Muhammad Haidar, p. 323
- Muhammad Haidar, pp. 329-330
- Muhammad Haidar, p. 326
- Muhammad Haidar, p. 330