The club had a difficult start to 2004-05 with the club ranked in the bottom in the league. The home wins against Espanyol, Athletic Bilbao, Valencia and Real Madrid, followed by the sole away win of the season against Athletic Bilbao, saw Getafe rise to 13th place, being the only team promoted to not be relegated. In the final stages of the season the club was able to lose the head manager Quique Sanchez Flores as well as a number of athletes to other clubs. In the following season it briefly topped the league before falling to finish in the ninth spot. At the tournament of 2006 FIFA World Cup, Argentine-born Mariano Pernia became Getafe's first ever Spanish international before transferring towards Atletico Madrid.
The 2006/07 season saw Getafe continued to finish ninth on the table. They conceded just 33 goals over 38 games. Goalkeeper Roberto Abbondanzieri was awarded the Zamora Trophy, having recorded 12 clean sheets. The most memorable part of the season was making it to in the 2007 Copa del Rey final, the competition where Getafe was not in the quarter-finals prior to. It was a two-legged semi-final with Barcelona where Getafe lost the first match 5-1 at the Camp Nou[19after which they won an 4-0 win in the second game in the Coliseum Alfonso Perez. Getafe fell in their first major final by 1-0 against Sevilla on the Santiago Bernabeu Stadium. The club was qualified for next year's UEFA Cup qualification, as Sevilla had already been able to qualify for UEFA Champions League through their league position.
The next season the following season, coach Bernd Schuster resigned after two years to become the head coach at Real Madrid, and Getafe named Michael Laudrup as his replacement. Under Laudrup's leadership, Getafe again finished the league in the middle of the table. For the UEFA Cup, the team made it to the quarter-finals after finishing on top of Group G with only one loss and setting up a match with four-time European Cup winners Bayern Munich. Getafe was able to draw the away match 1-1 because of an injury time equaliser scored by Cosmin Contra. In the second game, Ruben de la Red was sent off after just six minutes. Contra scored to put Getafe ahead shortly before half-time however, at the end of the 90th minute Franck Ribery scored to force the match into extra time. Two goals in quick succession from Javier Casquero and substitute Braulio made it Getafe an advantage of 3-1, however, Bayern came back with a goal by Luca Toni, before Toni scored again just prior to the end of extra time, which gave Bayern an away goal win. Getafe also made it to the final during the Copa del Rey, reaching the final for the second time. In the final at Vicente Calderon Stadium Vicente Calderon Stadium, Getafe lost 3-1 to Valencia.
In the 2015-16 season Getafe were sent to second division following 12 years in their first season. In the 2016-17 season the club was able to return back to La Liga after defeating Huesca and Tenerife to be promoted via the play-offs. In the 2017-18 season, Getafe ended up 8th without a hitch, and avoided the possibility of demotion back in the Segunda Division.