The mosque was built in 1442 (although it incorporated older structures dating back to 996)[citation needed] by Saqsiz Mirza, the elder of two sons of Amir Sayyid Ali, to commemorate his ancestors.

[3] On 9 August 1933, Chinese Muslim General Ma Zhancang killed and beheaded the Uyghur leader Timur Beg, displaying his head on a spike at Id Kah mosque.

[8][9] In April 1934, the Chinese Muslim general Ma Zhongying gave a speech at Id Kah Mosque in Kashgar, telling the Uyghurs to be loyal to the Republic of China Kuomintang government of Nanjing.

Radio Free Asia reported in 2018 that a plaque containing Quranic scriptures, which had long hung outside the front entrance of the mosque, had been removed by authorities.

[27][28][29] Henryk Szadziewski from the US-based Uyghur Human Rights Project told Radio Free Asia that while the mosque remains standing, "its disappearance would cause outrage given its importance.

"[30] According to Uyghur imam Ali Akbar Dumallah, who fled China in 2012, scenes of small groups of people praying at the Id Kah and other mosques are staged by the government for visitors.