2001–02 would see Baraja's first trophy win, where his goals late in the campaign helped Valencia to their first La Liga title in 31 years – he finished as team top scorer in the league, netting seven in only 17 league games after recovering from a knee injury. 2003–04 was another big year, winning both the domestic championship (with eight league goals from him) as well as the UEFA Cup, beating Olympique de Marseille 2–0 in the final.