At the same time the JUI was distrustful of Zia's close ties with the Jamaat-e-Islami and joined the anti-Zia and PPP-led Movement for the Restoration of Democracy (MRD).

[5] Following the death of Mufti Mehmood Ahmed in 1980, this dual relationship with Zia's regime eventually led to a split in the party which came to be divided into the JUI-F, headed by Maulana Fazal-ur-Rehman and the JUI-S headed by Samiul Haq, who supported supporting Jihadism and a totalitarian state and also Zia's regime and was a member in his parliament, the Majlis-e-Shura.

[6][8][9][10][11] Sami-ul-Haq was also a founder of Difa-e-Pakistan Council[12] and also a founding member of a six-party religious alliance Muttahida Majlis-e-Amal ahead of 2002 general elections.

[13][14] JUI-S remained allied with Muttahida Majlis-e-Amal until 2017 when it formed political alliance with Imran Khan's Pakistan Tehreek-e-Insaf.

[23][24][25] Its madrassa organization is Darul Uloom Haqqania, a Deobandi Islamic seminary which is the alma mater of many prominent Taliban members.