Valencia began the 1999-00 campaign with another victory The Spanish Super Cup, beating FC Barcelona. Valencia was second in the competition, just four points behind Champions Deportivo de La Coruna and just a few points behind the second-placed Barca. However, the most notable achievement was the UEFA Champions League; for the first time in the history of the league, Valencia reached the European Cup final. In the final, which took place in Paris on May 24, the year 2000 Real Madrid beat Valencia 3-1.
Claudio Lopez was also able to say departure, since he had signed with the Italian club Lazio and also to leave Farinos in the direction of Internazionale along with Gerard in the case of Barcelona. The major signings of this summer included John Carew, Ruben Baraja, Roberto Ayala, Vicente Rodriguez and the Brazilian left-back Fabio Aurelio. The other player that was bought included Pablo Aimar in January. Baraja, Aimar, Vicente and Ayala were soon to become a mainstay of Valencia's dominance during the 2000s early during La Liga.
Valencia began the tournament in a good way and finished at the top of the table after just 10 games. Following the break over Christmas However, Valencia started to pay for the highest price of a highly competitive competition such as that of the Champions League requires. After completing the mini-league stages Hector Cuper's team defeated Arsenal in the quarter-finals as well as Leeds United in the semi-finals and were set to take on Bayern Munich in the big final. Valencia was in the two European Cup finals in a sequence. The final was scheduled to take place on the streets of Milan on the San Siro on 23 May. Gaizka Mendieta provided Valencia the lead after scoring from the penalty spot at the beginning of the game. Goalie Santiago Canizares then stopped a penalty by Mehmet Scholl, however Stefan Effenberg drew level after the break, thanks to a second penalty. In extra-time, the game was a penalty shootout, and the Mauricio Pellegrino mistake earned Bayern Champions League glory and gave Valencia another exit from the finals. Valencia fell to fifth within La Liga and out of Champions League contestation for the 2001-02 season. In the final match of the year, it saw Valencia could only drawing at Camp Nou against Barcelona to ensure Champions League qualification. Los Che lost to Barcelona 3-1 on Barcelona 3-2 at the Nou Camp, with a late goal by Rivaldo that resulted in Barcelona being able to participate in Champions League qualification. Champions League while Valencia missed out.
President, D. Pedro Cortes was forced to resign for personal reasons and left the club in the month of July with the pleasure of winning one Copa del Rey, one Spanish Super Cup, and having finished runners-up twice in consecutive Champions League finals. D. Jaime Orti replaced as president, and he stated his determination to maintain the winning form that earned the club such a favourable reputation in the European circuit. There were some changes to the team and staff. Rafael Benitez, after helping CD Tenerife to promotion, was appointed coach Hector Cuper after the latter was appointed manager of Internazionale located in Italy. In the team, Gaizka Mendieta Didier Deschamps Luis Milla, and Zlatko Zahovic have all left, and Carlos Marchena, Mista, Curro Torres, Francisco Rufete, Gonzalo de los Santos and Salva Ballesta arrived.
From 1999 to the final season of 2004, Valencia had one of the most successful seasons during the span of the club's existence. With 2 La Liga titles, one UEFA Cup, one Copa del Rey in addition to an UEFA Super Cup in those six years, not less than five first-class championships as well as the two Champions League finals had been accomplished.
The first game they played against the champions Real Madrid produced a significant and significant victory. It was followed by the record-breaking 11 consecutive games won which broke the record that was set in the season 1970-71 in which they previously been crowned their La Liga title under Alfredo Di Stefano.
After losing at A Coruna against Deportivo on the 9th December 2001 The team needed to beat RCD Espanyol in the Estadi Olimpic Lluis Companys in order to avoid getting further behind league leaders. Valencia were down 2-0 at half-time, however an incredible comeback in the second half resulted in Valencia beat RCD Espanyol 3-1.
In the second half in the league, the team of Benitez was a bit shaky after losing 1-0 at Santiago Bernabeu to Real Madrid, but they bounced back and scored four wins and two draws over the next six games with UD Las Palmas Athletic Bilbao, Deportivo Alaves, Real Zaragoza, and Barca.
In one of the crucial games they'd be up with Espanyol, Valencia were trailing by 1-0 at half-time, and one man down after the expulsion of Carboni and after two goals scored by Ruben Baraja Valencia were able to win 2-1. In addition, the defeat of Real Madrid in the Anoeta derby in the relegation battle against Real Sociedad left Valencia with three points in on top.
It was the final match of the season. took place in La Rosaleda to face Malaga CF on May 5, 2002. This date will be remembered in the history of Valencia. The team hid in Benalmadena close to the venue of the match in order to gain concentration. A first goal by Roberto Ayala and another close to half-time by Fabio Aurelio secured the team that they would win their 5th La Liga title, 31 years after their previous victory.
It was a dismal one for Valencia The club did not succeed in their quest to keep their La Liga title and ended being outside their Champions League spots in fifth in the table, just behind Celta of Vigo. The team was also eliminated in the quarterfinals of the Champions League by Internazionale on away goals. This season, 2003-04 saw Valencia being a little behind the leaders of the past, Real Madrid. In February, following 26 games played Real Madrid were eight points in front. However, their form began to decline towards the end of the season and they were beaten in their final five games of the season and allowed Valencia to catch them and take the title. Valencia included an additional trophy UEFA Cup to this success. Valencia had been La Liga champions twice in three seasons.
At the end of summer 2004 the coach Rafael Benitez decided to leave the club, saying there were issues with the club's president. He was soon to be the director of Liverpool. The manager was later replaced the former Valencia manager Claudio Ranieri, who had recently been fired by Chelsea. The second time he was at Valencia was not a success However, Valencia were hopeful of winning the La Liga crown but, by February, they were in seventh position. Valencia was also eliminated from the Champions League group phase, which led to Ranieri getting sacked in February. The 2004-05 season came to an end with Valencia being left out of UEFA Cup spots.
The summer of 2005 saw Getafe CF coach Quique Flores was named Valencia's new coach. Valencia and finished the season in third position which earned Valencia an entry into the Champions League after a season out of the competition. In 2006, the season filled that was not without its challenges, a season that began with realistic expectations of a chance to compete in the race for La Liga was shattered by an extensive list of injury to players, as well as internal disputes between Flores and the new Director of Sporting Amedeo Carboni. Valencia finished the season fourth and was eliminated from the Champions League at the quarter-finals stage by Chelsea 3-1 on aggregate after edging out Italian champions Inter in the second round. At the end of summer 2007 the internal conflict of Flores as well as Carboni was settled , with Carboni becoming replaced Angel Ruiz as the new Sporting Director of Valencia.
On the 29th of October, 2007 The Valencia Board of Directors dismissed Flores after a string poor performances. The the interim manager Oscar Ruben Fernandez took over temporarily until a permanent manager could be discovered, believed to be Marcello Lippi, or Jose Mourinho. The next day, Dutch manager Ronald Koeman announced that he was leaving PSV to join Valencia. However, there was no change; in actual, Valencia even went on to fall to the 15th place within the League, only two points clear of the zone of relegation. However, on the 16th of April in the year 2008 Valencia took home the Copa del Rey by winning 3-1 win against Getafe on the Vicente Calderon Stadium. It was Valencia's seventh Copa title. The following day, following an utterly devastating defeat to the league to Bilbao, Valencia fired Ronald Koeman and took over the role of Voro who would take over Valencia as the Caretaker Manager for the remainder of the season. Voro would go to win his first game since the dismissal of Koeman and beat CA Osasuna 3-0 in his first game as the new manager. Voro was able to pull Valencia from the battle for relegation to a secure middle-table position of 10th and finally end an unsatisfactory league season with Los Che.
Highly highly rated Unai Emery was named Manager of Valencia on the 22nd of May, 2008. The beginning of the new manager's tenure appeared positive, with the club winning four of the first five matches, a rise that saw the team climb to the top in the La Liga table. Although they looked impressive throughout Europe, Los Che then suffered a shaky streak of performance in the league , which saw them fall to as low as seventh the table. There were reports of a huge internal debt to the club that was in excess of 400 million euros in addition to the fact that players were not paid for some time. The problems of the team were exacerbated after they were eliminated in the UEFA Cup by Dynamo Kyiv due to away goals. After a period that saw Valencia scored just five points in ten games within La Liga, an announcement was made that the team was able to secure an investment that would pay for the expenses of players until the final day of the year. The announcement was made in conjunction with an improvement in performance which saw the club win six of the following eight games, gaining back to the vital fourth Champions' League slot. But, Los Che were then defeated by rivals in fourth place Atletico Madrid, and Villarreal in the final three fixtures of this season and ended up finishing sixth in the table. This meant they were not able to get a second consecutive year in The Champions League.