[5] In 2002, known for his quick-release shooting and all-around presence, he, alongside Paul Artadi and Ronald Tubid, brought the Red Warriors to the Final Four after years of absence.

Eventually in the semifinals series, the Warriors lost to a much more defense-orchestrated team, the Far Eastern University Tamaraws led by tactician coach Koy Banal and star player Arwind Santos.

In 2001, he played for the ICTSI-La Salle Archers forming a backcourt tandem with Mike Cortez that almost had their team beating the veteran-laden Shark Energy Drink in the finals.

[10] The victory put the Purefoods team in a first-place finish in the classification phase, earning them an outright semifinals berth for the second consecutive time.

On June 1, 2007, Yap scored a career-high 41 points in a 109–97 win over the Welcoat Paints, leading Purefoods to a spot in the wildcard phase of the 2007 PBA Fiesta Conference playoffs.

Despite failing to deliver the win for his team, Yap's efforts equaled former PBA player Nelson Asaytono's record of scoring 40+ points in back-to-back games.

By the end of the 2007–2008 season, Yap averaged 21.32 ppg, 1.58 apg, 4.06 rpg, 0.76 spg and 0.24 blocks per game (bpg) in 37 minutes playing time.

He also won his second MVP award, for the 2009–2010 PBA season with averages of 17.98 ppg, 3.50 rpg, 2.02 apg and 0.64 spg while playing almost 34 minutes per ball game.

[17] Starting the 2010 Fiesta Conference, the team changed its name from Purefoods Tender Juicy Giants to B-Meg Derby Ace Llamados.

The end of the season, however, marked the departure of coach Ryan Gregorio, who left the Llamados after seven years and signed a deal with PBA returnee Meralco Bolts.

The two-time MVP and Peter June Simon led the team to the quarterfinals,[22] in which B-Meg scored back-to-back wins against the Meralco Bolts.

[24] Yap suffered breathing difficulties and struggled with his shooting in Game 2,[25] scoring 13 points in 31 minutes, but still played a main role and came up with a game-winning steal in the final seconds of the last quarter that gave B-Meg an 88–87 victory.

[41] After losing 84–93 in a seeding playoff against Ginebra (the Kings also finished the elimination round with a 6–3 record) for the 2nd spot, in which Yap scored 18 points but was held scoreless in the last quarter, the Llamados found themselves pitted in the quarterfinals against the Meralco Bolts.

[48][49] The B-Meg Llamados booked a ticket to the 2012 PBA Governors' Cup finals against the Rain or Shine Elasto Painters, after beating Ginebra 74–72, via a Peter June Simon game-winner.

With Game 7 at hand, B-Meg aimed to become just the fourth team in PBA history to come back from a 1–3 deficit in the finals – a feat they had previously accomplished in 2006.

On December 21, Yap led his team to a 106–82 victory in Game 2 over the Elasto Painters as he scored 34 points including 7 triples in 47 minutes of play, to help equalize the series 1–1.

With the help of Yap and Bowles' performances, San Mig ended the classification phase with a record of 8–6, fourth overall in the standings, which gave them an outright quarterfinal slot.

With a twice to beat advantage, San Mig eliminated the Alaska Aces in two games in the quarterfinals; the team then ousted the Meralco Bolts in the semifinals and faced the Boosters in the finals.

With the objective of winning a rare Grand Slam, the San Mig Coffee Mixers entered the 2014 Governors' Cup as defending champions, having won the previous year.

[68][69] Despite playing limited minutes and averaging career lows in most statistical categories for much of the season, in the finals, Yap further proved his reputation as a "clutch player" and helped his team win with many crucial shots in multiple games.

The Hotshots took their spot in the quarterfinals by defeating their last opponents Barako Bull Energy and Meralco Bolts, but fell in ranking due to a quotient system and were not given a twice to beat advantage.

On October 13, 2016, James Yap was sent to Rain or Shine Elasto Painters on a blockbuster trade in exchange for star point guard Paul Lee that led to a shocking reaction from the basketball fans.

In his very first game with the Elasto Painters on November 30, 2016, Yap made two 3-point shots to become the 6th player with at least 1,000 3-point conversions joining Jimmy Alapag (1,250), Allan Caidic (1,242), Ronnie Magsanoc (1,171), Dondon Hontiveros (1,119) and Al Solis (1,000).

[80] In the recently concluded 2018 PBA Commissioners' Cup, Yap towed the team to its first-ever semifinal appearance under coach Caloy Garcia where he had a career resurgence winning two Best Player of the Game citations, the first during their quarterfinal series-clinching victory over Globalport where he scored 27 points marked by 7 three-pointers made[81] and the second during Game 2 of their semifinal series with eventual champions Barangay Ginebra San Miguel where he scored 18 points with 3 rebounds.

[84] In the on-going 2019 PBA Philippine Cup, Yap's resurgence is in full display through the team's first eight games as he leads Rain or Shine in scoring with a 14.75 ppg average adding 2.88 rpg, 1.63 apg and 0.75 spg.

In the current 2020 PBA Philippine Cup being held in a bubble at the Angeles University Foundation (AUF) Sports Arena and Cultural Center in Pampanga, Yap moved into a tie for third place in the All-time List for Most 3-point shots converted with 1,171 after going 4/7 in Rain or Shine's game against the TNT Tropang Giga on November 10, 2020.

[89][87] In their last game in the eliminations against the Phoenix Fuel Masters held on November 11, 2020, Yap drilled a 3-pointer at the 10:58 mark of the third quarter as he officially broke his tie with former PBA great Magsanoc for sole third place in the all-time list as he now has 1,172 3-PT conversions.

[90] On January 23, 2022, Yap signed a contract extension with the team until the end of the 2021 season, but did not play a game as he was officially on a leave of absence due to him pursuing politics.

[100] In the 2009 Southeast Asia Basketball Association (SEABA) Championships, Yap was a member of the Powerade-Team Pilipinas that won the said tournament, beating Indonesia in the finals, 98–68.

[101] Yap declined the invitation to join the Smart Gilas 2.0 National Team Program including other SMC players like Arwind Santos, Marc Pingris and Alex Cabagnot because of personal reasons.