Born in Tashkent in a family of ulama who traced their lineage to Ahmad Yasawi, Babakhan studied at the Mu-yi Mubarak madrasa, where his father was mudarris.
Among his other teachers was Shami Domla, who in the 1920s presided over regular gatherings of local ulama where hadith was discussed.
Shami Domla posited the supremacy of hadith over all other sources of authority in questions of theology and law.
Ishan Babakhan was elected mufti of Spiritual Administration of the Muslims of Central Asia and Kazakhstan (SADUM) when the latter was established in 1943.
He died on June 5, 1957, at the age of 99 and was buried in the mausoleum of Kaffal Shashi in Tashkent by the decision of the government of the Uzbek SSR.