Yap entered the 2004 PBA Draft, and was selected as the second overall pick by the Purefoods Tender Juicy Giants. Bothered by an ailing shoulder, Yap had a slow start in the 2004-2005 season. Later on, he simprove as he had numerous games of which he scored 20 or more points. However, the Purefoods failed to get past the quarterfinal round against the Shell Turbo Chargers. Eventually, he lost to Rich Alvarez in the Rookie of the Year race. In the 2005-06 Fiesta Conference, Yap was 4th in the statistical race, behind at the end of the semifinals series, while the Giants finished 4-2 at the series conclusion. In the classification round of the Philippine Cup, he recorded 34 points against the Sta. Lucia Realtors then had a career-high 37 points to beat Barangay Ginebra Kings. Near the end of the round, he played an important role in the win against the powerhouse team Talk 'N Text. The victory put the Purefoods team in a best-of-seven semifinals slot.
After the accumulation of player statistics at the end of the semis, Yap edged out teammate Kerby Raymundo and Red Bulls' Jet Lemuel Salazar for the Philippine Basketball Association Most Valuable Player award. This made him, at 24 years of age, the fifth youngest players, and second sophomore to have won the individual award. He was the statistical leader and garnered more than 7000 combined votes from players, the 4-man committee, and the media, almost 5000 votes ahead of the rest of the candidates. He was also named to the Mythical First Team alongside teammates Raymundo and Roger Yap, and on-court rivals Enrico Villanueva and Lordy Tugade. In the 2006-07 season, he had back-to-back 40-point games against Welcoat and Coca-Cola.
Purefoods swept Alaska, 4-0, to be crowned 2009-2010 PBA Philippine Cup champions. For leading his team to this incredible feat, Yap was named Best Player of the Conference (BPC), as well as Finals MVP. He also won his second MVP award, for the 2009-2010 PBA season,.,JAMES YAP IS NOT A GAY.,/
