The other faction, the much smaller JUI-S, led by Samiul Haq, is of regional significance in Khyber Pakhtunkhwa.

The JUI traces its roots to politically active Deobandi who formed the Jamiat Ulema-e-Hind (JUH) in 1919 in British India.

The JUH was against colonialism and for a united India, opposing the formation of a separate homeland for Indian Muslims.

[10] JUI's first president, Shabbir Ahmad Usmani, broke away from the party in 1947 to form the Markazi Jamiat Ulema-e-Islam (MJUI), which played a key position in the passage of the Objectives Resolution of 1949 that laid down the "Islamic" foundations of future constitutions in Pakistan.

Under Mufti Mahmood during the 1960s the party "developed a strong presence" and base of support among the "intensely conservative countryside" of Balochistan and Khyber Pakhtunkhwa.

During the 1980s, the JUI supported some of General Zia ul Haq's policies, including his anti-Soviet Jihad in Afghanistan.

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).

[11] Following the death of Mufti Mehmood Ahmed in 1980s, 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 Zia and was a member in his parliament, the Majlis-e-Shura.

Both factions of the JUI have a large network of madrassas and mosques that provide the main basis for its religious activism and politics.

[15] About 30,000 Afghan students from JUI-controlled madrassas (both JUI (F) and JUI-S) in Pakistan joined the Taliban movement in Afghanistan.

The JUI (F) has also played a role in brokering peace deals between the military and militants in Pakistan's tribal belt.

The JUI (F) was also part of the current ruling PPP coalition but left the government amidst charges of corruption against one of its members, and information technology minister of the federal cabinet.

For example, following the 2 May 2011 U.S. raid in Abbottabad that led to Osama bin Laden's killing, the JUI (F), and the JUI-S participated in a multi-party conference in Peshawar, condemning the drone strikes and calling on the government to end logistical support to NATO troops in Afghanistan.