This is the first season without the PCU Dolphins who have taken an indefinite leave of absence after several of their juniors' division players were found to have used falsified documents to enter the school.

[1] The games began on June 27 at the Araneta Coliseum with an opening ceremony led by San Beda, with a keynote speech by United States Ambassador to the Philippines Kristie Kenney, culminating with a tripleheader with season host San Beda Red Lions routing the Mapua Cardinals 82–55 in the opening game.

In the men's division, the San Sebastian Stags had an all-time league-best 15-game winning streak, ending on their second-round game against the Letran Knights.

In the juniors' division, the Letran Squires had a 17-game winning streak, only for them to be beaten by the San Beda Red Cubs in the last game of the elimination round.

The Red Cubs blew out the Squires in the playoff for #1, but both teams did not need their twice-to-beat advantage to eliminate the JRU Light Bombers and the San Sebastian Staglets respectively in the semifinals.

In the deciding game, San Beda pulled away late in the fourth quarter after Letran cut down the 15-point lead to two points to give retiring coach Ato Badolato his 15th juniors' championship.

The NCAA originally wanted to play in the Rizal Memorial Coliseum "But it's still under repair so maybe next year," management committee chairman Jose Mari Lacson of San Beda College said.

JRU and Benilde remained unbeaten, winning against UPHSD and Mapua respectively to join Arellano and San Sebastian at the top of the standings with a 2–0 slate at the end of the first week of competition.

San Beda dealt Arellano their first loss at the start of week 2, with the Great Danes winning their first game against fellow guest school EAC.

San Sebastian and JRU continued their unbeaten runs; the Stags defeated the Chiefs, and the Heavy Bombers blowing out the Great Danes.

Perpetual Help won against Mapua, but before losing to the Chiefs, while San Beda and Letran held off separate opponents, with the Knights needing an extra period to ward off the Generals.

Meanwhile, San Sebastian was taken by Mapua to the limit before losing by three points, to set up an anticipated game against arch rival Letran at the first round finale.

In the first round finale, Letran led for majority of the game, even by as much as ten at halftime, before the Stags staged a third quarter rally to lead by double digits.

The Knights clawed through, and had a chance to extend the game into overtime, but Kevin Alas' off-balanced three-pointer rattled in and out of the rim as time expired to give San Sebastian their first first round sweep since their 1997 championship run.

San Beda and JRU still maintained the second and third places in the team standings with easy wins against doormats Angeles University Foundation and Mapua; both losing schools were eliminated from semifinals contention.

San Beda and JRU ended the week how it started, with easy wins against Perpetual Help and Arellano respectively, giving the two teams tickets to the semifinals.

[16] EAC avenged their first round loss against AUF with a double-digit win, with Letran had another fourth quarter run to pull away against UPHSD in the endgame.

In the week's last pair of games, Mapua hands Letran the last semifinal berth with a double-digit upset against the Chiefs, while CSB ends their 6-game losing streak with an easy win against AUF.

With the resumption of games on October 2 a week after the tropical storm hit, games resumed but not after a moment of silence was observed commemorating all victims of the typhoon, including Philippine Basketball Association team Barako Bull Energy Boosters manager and former Letran Squires football player Tony Chua, who died in the height of the storm.

Meanwhile, San Sebastian clinched the twice-to-beat advantage in the semifinals with a win over JRU, which won their last game of the season against EAC with a 36-point rout to end their elimination round campaign with a win; the Generals ended tied for sixth and presumably holds the tiebreakers against Mapua and CSB and can clinch the NCAA's last zonal berth in the 2009 Philippine Collegiate Championship.

However, on July 27, 2009, ABS-CBN, through UHF channel Studio 23 did not air the scheduled NCAA games to give way for the State of the Nation Address of President Gloria Macapagal Arroyo.