Pakistan Football Federation was created on December 5, 1947. Mohammad Ali Jinnah became the Patron-in-Chief of the PFF. In 1948, the PFF became affiliated with FIFA. It is also one of the founding members of the Asian Football Confederation when it was established in 1954. PFF organised the first National Championship in 1948 at Karachi.

The Preamble of the constitution of PFF says it is the duty of the PFF, "i) To administer, govern, organise, control and promote the game of Football, and, ii) To provide a general code for the Conduct of Provincial Football Associations, Units, Leagues, Institutions, Government Departments, Banks, Armed Services, Clubs, etc, associated with the game of Football in Pakistan."

On paper, there is a PFF National Football Development Programme under which Pakistan School Football System operates.

According to PFF, "In 2004, the PFF devised a new structure for National Soccer on advice of FIFA and AFC, introducing A and B Leagues -- Pakistan Premier League (PPL) and PFF League. In 2006, National Club Championship was introduced at Lahore, a C-Division event of PFF.

The PFF governs all football clubs in Pakistan. It is a member of AFC and FIFA. All of Pakistan’s football clubs must be members of the PFF. The PFF is responsible for the appointment of the management of the Pakistan men’s and women’s national teams and the organisation of the Pakistan Premier League (the top division), and other lower divisions.

The game is controlled at the local level by 8 provincial football federations affiliated to the PFF but with responsibilities for organising and running football activities in their area like Islamabad football association.

In August 2003, the PFF was under new management, as Makhdoom Syed Faisal Saleh Hayat took over as President of PFF.

With the Assistance of FIFA, the PFF set up a national football league in 2004, which is now called the Pakistan Premier League. In 2005 a National Championship was set up for women’s football.

In 2007, the inter-city Geo Super Football League was established, making it the first time that Pakistani club football was telecast live on national television via GEO Super. It also became Pakistan’s first professional football tournament.

Pakistan’s core national league has three divisions. The National Football Championship is named as the Pakistan Premier League (PPL) while National Championship is known as the Pakistan Football Federation League (PFF league) and the National Club Championship (C-Division) is the lowest division. Below this are regional leagues likes IFA in Islamabad. There is also a national knock-out competition called the National Football Challenge Cup.

Critics of the PFF believe bureaucratic inefficiencies and politics within the PFF machinery have hindered growth of this game in Pakistan.