In mid-July 2011, Chelsea manager André Villas-Boas confirmed that the Blues had agreed a deal with Genk for the young goalkeeper, stating "There is an agreement between the two clubs... It is also subject to personal agreements and from then we will decide what is best for him." Having signed for a fee that could rise to a reported £7.9m, Courtois joined Atlético Madrid on a season-long loan a few days later. Courtois joined Atletico Madrid on loan in August 2011 soon establishing himself as first choice at the Vicente Calderón. He made his La Liga debut on 28th August 2011 against Osasuna – keeping a clean sheet in a 0-0 draw – before his run of games was ended with a red card in a match against city rivals Real Madrid. He soon re-established himself and continued to impress, helping Atlético to fifth place in La Liga. To crown an impressive first season in a top European league, Courtois kept yet another clean sheet in Atlético's 3-0 triumph over fellow La Liga side Athletic Bilbao in the Europa League Final on Thursday 9 May in Bucharest, two days before his 20th birthday.
On 27 June 2012 Atlético Madrid confirmed that Courtois' loan had been extended for a further season.
He began the 2012-13 campaign with a victory against his parent club in the UEFA Super Cup in Monaco, before going on to a record-breaking La Liga campaign. He broke the record for most consecutive minutes without conceding a league goal at home and followed that up by doing the same for the away landmark. He finished as comfortable winner of the 'Zamora' award for the most clean sheets in the league with 20, and made two world-class saves in the Final of the Copa de Rey where Atlético beat Real Madrid 2-1 to secure their first domestic trophy in 16 years and a first Madrid derby win in 14.
In June 2013 it was confirmed that Courtois would spend a third season on loan at the Vicente Calderón.
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