Cika wannan jumla: An ba da rancen Courtois ga Atlético don rufe kakar 2012-13. Wasansa na farko na karin lokacin da aka ba shi ya kasance da kungiyar Chelsea a cikin
2012 UEFA Super Cup karshe a Monaco, wanda ya ƙare a 4-1 nasara ga Atlético Madrid. Daga baya a cikin kakar wasa, Courtois ya kafa sabon rikodin Atlético Madrid na mintuna 820 ba tare da cin kwallo a Estadio Vicente Calderon ba, wanda ya ƙare ta hanyar shan kashi a cikin asarar 1-0 ga Real Sociedad. Atlético ta kai wasan karshe na Copa del Rey na 2013, kuma an zabi Courtois a matsayin dan wasan wasan a wasan da suka yi nasara da Real 2-1, karo na farko da Atlético ta doke abokan hamayyarsu a cikin shekaru 14.