Unable to cement a starting place, his best output being 26 matches during 1997–98 (but he lost his place in the final part of the year to Bodo Illgner, thus missing the 1998 Champions League final), Cañizares moved to Valencia CF in 1998 to replace the retired Andoni Zubizarreta. He helped the club to win the Spanish Cup and Supercup finals in 1999, also reaching consecutive UEFA Champions League finals (2000 and 2001, saving a penalty from FC Bayern Munich's Mehmet Scholl in normal time of an eventual penalty shootout defeat in the latter edition) and winning national championships in 2002 and 2004, adding the UEFA Cup and Supercup 2004 finals; following the latter campaign, the 34-year-old renewed his contract with the "Che" for a further two years.