The football body's origins dates back to 1907 when it was established as the Philippine Amateur Football Association (PAFA). It was among the twelve founding Asian football associations of the Asian Football Confederation.
In 1917, the first Spanish and Filipino footballer to play for a European club, Paulino Alcántara Riestra, was selected by the Philippines to represent the country at the Far Eastern Championship Games in Tokyo. He helped them defeat Japan 15–2, which remains the largest win in Philippine international football history.
In 1961, stakeholders of Philippine football officially organized themselves to establish the Philippine Football Association (PFA) which was later reorganized as the Philippine Football Federation in 1982.
On October 1996, Rene Adad was installed as PFF president after a snap election which ousted his predecessor, Ricardo Tan. In 2002, the PFF inaugurated its first regional center in Barotac Nuevo, Iloilo.
Mari Martinez three year administration as PFF President has been controversial. On his first year as President in 2007, he summarily dismissed Jose Mari "Jojo" Rodriguez and Richard "Ritchie" Gannaban from their positions as Deputy General Secretary and Executive Secretary, respectively, when the two discovered Martinez's mishandling and misappropriation of PFF funds. The two filed a case against PFF and Martinez for their summary dismissal with the National Labor Relations Commission (NLRC) of the Department of Labor and Employment (DOLE). The NLRC decided in their favor and ordered the PFF to pay damages.
In the same year, there was also an attempt to remove Martinez from office. However this move was halted when several members of the opposition decided against pursuing for Martinez's ouster, following a guest appearance by then Asian Football Confederation President Mohammed bin Hammam who announced a gift donation to the PFF amounting to ₱10 million. This move was viewed as a bribe by critics of Martinez.
In 2009, a crisis affected the Philippine women's national futsal and men's national football teams which saw the ouster of women's futsal coach Emmanuel Batungbacal and long-time men's national football coach Juan Cutillas. Batungbacal was sacked by the PFF under recommendation from PFF Futsal Committee chairman Esmaeil Sedigh, from his position for sending an unsanctioned squad to futsal competition in New Zealand. Batungbacal described the move as "ironic" and showed documents to the media showing that the PFF indeed sanctioned his squad. He also accused Martinez of ignoring his pleas to express his concerns regarding the matter. The players who played under Batungbacal resigned from international duty as protests. Martinez said that Batungbacal was sacked due to lack of a coaching license and denied accusations that he ignored Batungbacal saying a dialogue between them already took place.
On November 27, 2010 at the PFF 7th Ordinary Congress at the PhilSports Complex in Pasig, Martinez was ousted by 25 Presidents out of the 29 present member associations to approve a resolution made by 8 members of the Board of Governors calling for the ousting and replacement of Martinez as PFF president. Martinez was accused and charged in court for falsifying public documents particularly when he notarized a Secretary's Certification with an individual by the name of Henry Tsai included as one of the signatories to the account of the federation in Banco de Oro and Bank of the Philippine Islands even if there was no motion to include Tsai as a signatory. Tsai was a former co-worker of Martinez at Soriamont Steamship Agencies, who was also named Managing Consultant of the PFF and later Executive Vice President. Martinez is accused of misusing funds of the federation amounting to ₱5 million, ₱4 million of which is unliquidated, which was designated to Tsai, for his own personal use and buying shares at the Valle Verde Country Club. Mariano Araneta was named Interim President.