Azhar later ousted PFF General Secretary Hafiz Salman Butt (a Member of National Assembly of Jamaat-e-Islami) in 1994 due to political rifts and alleged abuse of power.

[21] Under Hafiz Salman Butt, the 1992–93 and 1993–94 seasons of the National Football Championship structured on a proper league-style basis and spread over a number of months.

[22] Butt also managed to get a three-year sponsorship deal with Lifebuoy Soap, with amounts of 35 million PKR spent in the organisations of the seasons and televised through the country.

[18][25][26] With Butt's dismissal in 1994 and ban by FIFA in 1995, Pakistani football declined again into an era of mismanagement and long-lasting lack of sponsors in the upcoming years.

The Lahore High Court was forced to intervene in and ordered a stay on polling and appointed a temporary administrator until matters were resolved between the two factions.

[34] The PFF chairman Faisal Saleh Hayat said that the "Elections were approved by AFC, but the Asian governing body had no comment on the situation.

They concluded that Hayat be given a mandate for two years, in which he would have to amend PFF statutes and form an independent disciplinary committee before holding elections again.

[36][37] The Lahore High Court appointed administrator Asad Munir was given authority to manage football activity in Pakistan, while the two factions sorted out differences.

[38] In February 2017, the Lahore High Court reinstated Hayat as PFF president, with FIFA giving him until September 2017 to revise statutes and organize new elections.

[39][40] In July 2017, FIFA threatened to suspend the PFF's membership if it kept refusing to hand football affairs to its president-elect Faisal Saleh Hayat.

[47] Karachi United former captain Humza Khan was appointed as Normalization Committee for the Pakistan Football Federation in September 2019, whose task was to hold elections of the country's football governing body and bring it would bring an end to a four-year crisis that resulted in Pakistan suffering significantly in the game.

In January 2021, FIFA appointed Pakistani Canadian Haroon Malik as new chairman of the Pakistan Football Federation Normalisation Committee.

[17][52] On 27 March 2021, the PFF's office was attacked and people inside held hostage by its former president, Syed Ashfaq Hussain Shah, and his group, and the ongoing women's championship was cancelled.