Koubek returned to the Czech First League as the manager of Mladá Boleslav on 28 May 2011.[2] Koubek led Boleslav to fourth place in the 2011–12 Czech First League and qualification for the following season's UEFA Europa League. However, after a run of three consecutive league defeats, he resigned from his position in September 2012.[3] Koubek was appointed to the manager's position at Slavia Prague in September 2013 following the resignation of former boss Michal Petrouš.[4] He was sacked in March 2014.[5] In August 2014, he became the new manager of FC Viktoria Plzeň[6] and in May 2015 won his first league title. On 30 May 2016, Koubek was announced as the new manager of Bohemians 1905.[7] Koubek was appointed to the manager's position at Hradec Králové in June 2021 following the resignation of manager Zdenko Frťala.[8]
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