Stanislawski became interim manager of FC St. Pauli on 22November 2006 after Andreas Bergmann was sacked by the club. André Trulsen became the new manager, ending Stanislawski's reign as interim manager. Stanislawski returned as manager on 27 June 2008 after spending time in Cologne getting his coaching certificate. Stanislawski left at the end of the 2010–11 season in order to manage TSG Hoffenheim. Stanislawski spent 18 years at FC St. Pauli.
On 19 April 2011, TSG Hoffenheim announced he would become their new manager when the new season started. On 9 February 2012, he left Hoffenheim after having his contract terminated by club advisory board.