The NCAA was founded in 1924 on the initiative of Regino R. Ylanan, a physical education professor of the University of the Philippines (UP).

[3][4] The decision of the board of directors to file papers of incorporation with the then Bureau of Commerce in 1930 led to protests from the University of the Philippines, which was the only public institution among member schools, saying that it would lead to commercialization.

This led into the formation, via an Article of Agreement, of a triangular meet among NU, UP and UST, with the Board of Control's condition that NCAA events should take precedence.

Due to the home court advantage of the Ateneo, Blue Eagles' games were held on the old Rizal Memorial.

[7] The decade produced legendary collegiate players like Carlos Loyzaga (San Beda), Lauro "the Fox" Mumar (Letran), and Francisco Rabat (Ateneo) among others.

The opening of the Araneta Coliseum, the largest indoor arena in the Philippines, prompted the league to transfer the championship round there.

[8] Trinity College of Quezon City also joined in 1974, the league's golden anniversary, according to newspapers and other publications of that year.

[15] San Beda left the league in 1983, reasoning that the college focused on school-based sports activities like intramurals.

[8] With the withdrawal of Ateneo de Manila, league games returned to the old Rizal Memorial and to the PhilSports Arena, since the Loyola Center was now the location of the UAAP tournament.

Also with the withdrawal of the three founding members, most daily publications tagged the NCAA as "an ironic journey from sports to violence.

[4] Measures were taken to prevent major brawls from starting such as the patrolling by the respective faculties of the member schools, to control the behavior of the crowd were implemented as part of the remedy to ensure the security during the NCAA games.

[8] The addition of Philippine Christian University and De La Salle-College of Saint Benilde in the late 1990s brought the league membership to eight schools .

A major breakthrough occurred when the league, upon the initiative of host school San Beda, made a move that switched the television coverage of NCAA games from MCI group to ABS-CBN on March 18, 2002.

[19][20] In 1998, the affiliated schools in the Calabarzon region and southern Metro Manila established NCAA South, an offshoot of the league.

[28] Lyceum of the Philippines University (LPU), which had earlier sought membership, was accepted as a guest team in the Season 87 (2011–12).

The current president of the Policy Board is Jose Paulo Campos  the Emilio Aguinaldo College, while the Management Committee is headed by Estefania Boquiren Jr. of Emilio Aguinaldo College The number and composition of NCAA members has changed over the years.

The association is currently composed of the following colleges and universities, with their corresponding team names, affiliation, and year of admission.

The Policy Board, composed of the presidents of member schools, manages the NCAA's external and internal affairs.

The other main administrative body in the NCAA is the Management Committee (MANCOM), which determines matters of athletic concern, such as determining the proper conditions for playing, suspension of players, coaches, and referees, reversal or review of game results, and investigation of ineligible players.

The president of the Policy Board and the chairperson of the Management committee come from the school currently hosting the basketball tournament.

In the 87th season of the NCAA, cheerleading has been upgraded to a "regular sport" which means it will contribute points in the overall championship race.