Hrubesch was head coach of Germany's B team from 22 March 1999. He was appointed assistant coach of Germany's A team on 8 May 2000. The coaching staff was reconstructed on 26 March 2002 with Uli Stielike becoming the new head coach of Germany's B team. In 2008, Hrubesch won the European Championship with the Germany U–19 team. On 9 January 2009, Hrubesch was named interim coach of the Germany U–21 team. Rainer Adrion was unavailable to become the permanent head coach until the summer. In June 2009, he guided Germany to the final of the 2009 UEFA Under-21 Championships where they defeated England Under 21s by 4–0. On 11 November 2009, it was announced that he will begin to work as U-19 coach of the DFB. He returned to the Germany U–21 team after Rainer Adrion was sacked on 21 June 2013.